Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/inputs/xdr Working: n-5-33.cluster.ucsf.bkslab.org:/scratch/xiaobo/340664/xdr-8058097.96 Result: /scratch/xiaobo/340664/xdr-8058097.96 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xdr 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/xak/inputs/xdr mkdir: created directory `/scratch/xiaobo/340664' mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96' /scratch/xiaobo/340664/xdr-8058097.96 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/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/340664/xdr-8058097.96/working' mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/protonate' Storing results in /scratch/xiaobo/340664/xdr-8058097.96/finished Working in /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 /scratch/xiaobo/340664/xdr-8058097.96/working/protonate /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Using inputs as protomers/tautomers. No processing done 492 substances and 1000 protomers extracted Coalesing and merging protomers 1000 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1000 protomers after new stereo-center expansion /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Bulk generating 3D conformations all protomers in /scratch/xiaobo/340664/xdr-8058097.96/working/3D mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/340664/xdr-8058097.96/working/protonate/xdr-protomers-expanded.ism /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' 1001 3D conformations generated for 1000 compounds Building ZINC001721137458 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building' mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721137458 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/1 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001721137458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721137458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721137458 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 9, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 17, 17, 37, 46, 46, 46, 46, 46, 46, 46, 14, 15, 15, 15, 15, 9, 9, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/2 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001721137458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721137458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721137458 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 36, 45, 45, 45, 45, 45, 45, 45, 14, 15, 15, 15, 15, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721137458 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/finished' Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 Building ZINC001721137458 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721137458 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 1) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001721137458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721137458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721137458 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 9, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 17, 17, 37, 46, 46, 46, 46, 46, 46, 46, 14, 15, 15, 15, 15, 9, 9, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 2) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001721137458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721137458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721137458 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 36, 45, 45, 45, 45, 45, 45, 45, 14, 15, 15, 15, 15, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721137458 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137458 Building ZINC001721137459 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721137459 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/3 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001721137459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721137459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721137459 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 36, 45, 45, 45, 45, 45, 45, 45, 14, 15, 15, 15, 15, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/4 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001721137459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721137459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721137459 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 10, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 18, 18, 37, 46, 46, 46, 46, 46, 46, 46, 15, 16, 16, 16, 16, 10, 10, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721137459 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 Building ZINC001721137459 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721137459 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 3) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001721137459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721137459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721137459 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 36, 45, 45, 45, 45, 45, 45, 45, 14, 15, 15, 15, 15, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 4) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001721137459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721137459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721137459 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 10, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 18, 18, 37, 46, 46, 46, 46, 46, 46, 46, 15, 16, 16, 16, 16, 10, 10, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721137459 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137459 Building ZINC001721137600 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721137600 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/5 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCN1CCOCC1) `ZINC001721137600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721137600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721137600 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 29, 29, 44, 44, 44, 44, 44, 19, 21, 21, 21, 21, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/6 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCN1CCOCC1) `ZINC001721137600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721137600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721137600 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 29, 29, 44, 44, 44, 44, 44, 19, 21, 21, 21, 21, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721137600 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 Building ZINC001721137600 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721137600 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 5) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCN1CCOCC1) `ZINC001721137600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721137600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721137600 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 29, 29, 44, 44, 44, 44, 44, 19, 21, 21, 21, 21, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 6) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCN1CCOCC1) `ZINC001721137600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721137600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721137600 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 29, 29, 44, 44, 44, 44, 44, 19, 21, 21, 21, 21, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721137600 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721137600 Building ZINC001721138142 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138142 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/7 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1OC) `ZINC001721138142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138142 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 31, 31, 46, 46, 46, 46, 46, 46, 46, 18, 19, 19, 19, 19, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/8 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1OC) `ZINC001721138142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138142 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 31, 31, 46, 46, 46, 46, 46, 46, 46, 18, 19, 19, 19, 19, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138142 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 Building ZINC001721138142 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138142 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 7) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1OC) `ZINC001721138142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138142 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 31, 31, 46, 46, 46, 46, 46, 46, 46, 18, 19, 19, 19, 19, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 8) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1OC) `ZINC001721138142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138142 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 31, 31, 46, 46, 46, 46, 46, 46, 46, 18, 19, 19, 19, 19, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138142 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138142 Building ZINC001721138147 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138147 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/9 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn2cccnc2n1) `ZINC001721138147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721138147 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 43, 43, 48, 48, 48, 48, 48, 48, 48, 48, 30, 31, 31, 31, 31, 18, 18, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/10 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn2cccnc2n1) `ZINC001721138147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721138147 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 43, 43, 48, 48, 48, 48, 48, 48, 48, 48, 30, 31, 31, 31, 31, 18, 18, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138147 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 Building ZINC001721138147 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138147 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 9) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn2cccnc2n1) `ZINC001721138147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721138147 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 43, 43, 48, 48, 48, 48, 48, 48, 48, 48, 30, 31, 31, 31, 31, 18, 18, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 10) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn2cccnc2n1) `ZINC001721138147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721138147 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 43, 43, 48, 48, 48, 48, 48, 48, 48, 48, 30, 31, 31, 31, 31, 18, 18, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138147 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138147 Building ZINC001721138181 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138181 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/11 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCNC1=O) `ZINC001721138181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138181 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 30, 19, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 39, 40, 40, 40, 40, 40, 40, 40, 40, 36, 40, 40, 40, 40, 19, 19, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 222 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/12 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCNC1=O) `ZINC001721138181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138181 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 31, 20, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 39, 41, 41, 41, 41, 41, 41, 41, 41, 38, 40, 40, 40, 40, 20, 20, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 208 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138181 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 Building ZINC001721138181 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138181 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 11) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCNC1=O) `ZINC001721138181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138181 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 30, 19, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 39, 40, 40, 40, 40, 40, 40, 40, 40, 36, 40, 40, 40, 40, 19, 19, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 222 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 12) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCNC1=O) `ZINC001721138181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138181 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 31, 20, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 39, 41, 41, 41, 41, 41, 41, 41, 41, 38, 40, 40, 40, 40, 20, 20, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 208 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138181 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138181 Building ZINC001721138182 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138182 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/13 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCNC1=O) `ZINC001721138182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138182 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 29, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 37, 39, 41, 41, 41, 41, 41, 41, 41, 36, 38, 38, 38, 38, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/14 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCNC1=O) `ZINC001721138182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138182 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 18, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 37, 38, 41, 41, 41, 41, 41, 41, 41, 34, 38, 38, 38, 38, 18, 18, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138182 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 Building ZINC001721138182 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138182 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 13) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCNC1=O) `ZINC001721138182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138182 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 29, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 37, 39, 41, 41, 41, 41, 41, 41, 41, 36, 38, 38, 38, 38, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 14) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCNC1=O) `ZINC001721138182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721138182 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 18, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 37, 38, 41, 41, 41, 41, 41, 41, 41, 34, 38, 38, 38, 38, 18, 18, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138182 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138182 Building ZINC001721138394 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138394 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/15 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(OC)no1) `ZINC001721138394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721138394 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(OC)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 12, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 21, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 37, 37, 49, 49, 49, 49, 49, 49, 22, 22, 22, 22, 22, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/16 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(OC)no1) `ZINC001721138394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721138394 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(OC)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 12, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 21, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 37, 37, 49, 49, 49, 49, 49, 49, 22, 22, 22, 22, 22, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138394 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 Building ZINC001721138394 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138394 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 15) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(OC)no1) `ZINC001721138394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721138394 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(OC)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 12, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 21, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 37, 37, 49, 49, 49, 49, 49, 49, 22, 22, 22, 22, 22, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 16) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(OC)no1) `ZINC001721138394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721138394 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(OC)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 12, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 21, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 37, 37, 49, 49, 49, 49, 49, 49, 22, 22, 22, 22, 22, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138394 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138394 Building ZINC001721138690 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138690 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/17 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1) `ZINC001721138690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721138690 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 18, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 35, 35, 43, 43, 43, 43, 43, 43, 43, 26, 28, 28, 28, 28, 18, 18, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/18 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1) `ZINC001721138690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721138690 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 18, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 36, 36, 44, 44, 44, 44, 44, 44, 44, 26, 28, 28, 28, 28, 18, 18, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138690 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 Building ZINC001721138690 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721138690 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 17) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1) `ZINC001721138690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721138690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721138690 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 18, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 35, 35, 43, 43, 43, 43, 43, 43, 43, 26, 28, 28, 28, 28, 18, 18, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 18) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1) `ZINC001721138690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721138690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721138690 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 18, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 36, 36, 44, 44, 44, 44, 44, 44, 44, 26, 28, 28, 28, 28, 18, 18, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721138690 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721138690 Building ZINC001721141188 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721141188 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/19 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cc(OC)no1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721141188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721141188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721141188 none CCN(CCNC(=O)c1cc(OC)no1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 8, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 11, 17, 38, 38, 38, 46, 46, 46, 46, 46, 46, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 17, 17, 38, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/20 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cc(OC)no1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721141188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721141188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721141188 none CCN(CCNC(=O)c1cc(OC)no1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 8, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 9, 15, 37, 37, 37, 46, 46, 46, 46, 46, 46, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 15, 15, 37, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721141188 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 Building ZINC001721141188 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721141188 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 19) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cc(OC)no1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721141188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721141188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721141188 none CCN(CCNC(=O)c1cc(OC)no1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 8, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 11, 17, 38, 38, 38, 46, 46, 46, 46, 46, 46, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 17, 17, 38, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 20) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cc(OC)no1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721141188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721141188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721141188 none CCN(CCNC(=O)c1cc(OC)no1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 8, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 9, 15, 37, 37, 37, 46, 46, 46, 46, 46, 46, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 15, 15, 37, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721141188 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721141188 Building ZINC001721142698 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721142698 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/21 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)C1CN(C(C)=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721142698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721142698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721142698 none CCN(CCNC(=O)C1CN(C(C)=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 10, 13, 16, 16, 16, 42, 42, 42, 50, 50, 42, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 13, 13, 16, 42, 42, 42, 50, 50, 50, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/22 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)C1CN(C(C)=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721142698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721142698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721142698 none CCN(CCNC(=O)C1CN(C(C)=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 10, 12, 13, 13, 13, 39, 39, 39, 48, 48, 39, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 12, 12, 13, 39, 39, 39, 48, 48, 48, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721142698 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 Building ZINC001721142698 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721142698 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 21) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)C1CN(C(C)=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721142698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721142698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721142698 none CCN(CCNC(=O)C1CN(C(C)=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 10, 13, 16, 16, 16, 42, 42, 42, 50, 50, 42, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 13, 13, 16, 42, 42, 42, 50, 50, 50, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 22) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)C1CN(C(C)=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721142698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721142698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721142698 none CCN(CCNC(=O)C1CN(C(C)=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 10, 12, 13, 13, 13, 39, 39, 39, 48, 48, 39, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 12, 12, 13, 39, 39, 39, 48, 48, 48, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721142698 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721142698 Building ZINC001721148054 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721148054 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/23 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CN2CCC1CC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721148054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721148054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721148054 none CCN(CCNC(=O)[C@H]1CN2CCC1CC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 15, 24, 45, 45, 45, 48, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 24, 24, 45, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/24 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CN2CCC1CC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721148054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721148054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721148054 none CCN(CCNC(=O)[C@H]1CN2CCC1CC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 15, 24, 42, 42, 42, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 24, 24, 42, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721148054 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 Building ZINC001721148054 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721148054 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 23) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CN2CCC1CC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721148054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721148054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721148054 none CCN(CCNC(=O)[C@H]1CN2CCC1CC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 15, 24, 45, 45, 45, 48, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 24, 24, 45, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 24) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CN2CCC1CC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721148054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721148054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721148054 none CCN(CCNC(=O)[C@H]1CN2CCC1CC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 15, 24, 42, 42, 42, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 24, 24, 42, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721148054 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148054 Building ZINC001721148055 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721148055 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/25 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CN2CCC1CC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721148055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721148055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721148055 none CCN(CCNC(=O)[C@@H]1CN2CCC1CC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 14, 22, 40, 40, 40, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 22, 22, 40, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 196 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/26 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CN2CCC1CC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721148055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721148055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721148055 none CCN(CCNC(=O)[C@@H]1CN2CCC1CC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 15, 24, 44, 44, 44, 48, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 24, 24, 44, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721148055 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 Building ZINC001721148055 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721148055 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 25) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CN2CCC1CC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721148055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721148055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721148055 none CCN(CCNC(=O)[C@@H]1CN2CCC1CC2)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 14, 22, 40, 40, 40, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 22, 22, 40, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 196 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 26) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CN2CCC1CC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721148055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721148055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721148055 none CCN(CCNC(=O)[C@@H]1CN2CCC1CC2)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 15, 24, 44, 44, 44, 48, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 24, 24, 44, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721148055 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721148055 Building ZINC001721152735 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721152735 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/27 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721152735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721152735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721152735 none CCN(CCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 7, 12, 19, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 19, 19, 28, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/28 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721152735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721152735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721152735 none CCN(CCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 8, 14, 21, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 21, 21, 29, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721152735 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 Building ZINC001721152735 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721152735 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 27) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721152735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721152735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721152735 none CCN(CCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 7, 12, 19, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 19, 19, 28, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 28) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721152735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721152735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721152735 none CCN(CCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 8, 14, 21, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 21, 21, 29, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721152735 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152735 Building ZINC001721152736 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721152736 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/29 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721152736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721152736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721152736 none CCN(CCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 8, 14, 21, 29, 29, 35, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 21, 21, 29, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/30 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721152736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721152736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721152736 none CCN(CCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 8, 13, 20, 28, 28, 34, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 20, 20, 28, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721152736 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 Building ZINC001721152736 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721152736 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 29) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721152736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721152736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721152736 none CCN(CCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 8, 14, 21, 29, 29, 35, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 21, 21, 29, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 30) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721152736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721152736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721152736 none CCN(CCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 8, 13, 20, 28, 28, 34, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 20, 20, 28, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721152736 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721152736 Building ZINC001721154810 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721154810 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/31 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]1(CC)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721154810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721154810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721154810 none CCN(CCNC(=O)[C@@]1(CC)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 12, 18, 31, 31, 37, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/32 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]1(CC)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721154810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721154810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721154810 none CCN(CCNC(=O)[C@@]1(CC)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 12, 18, 33, 33, 38, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 18, 18, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721154810 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 Building ZINC001721154810 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721154810 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 31) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]1(CC)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721154810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721154810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721154810 none CCN(CCNC(=O)[C@@]1(CC)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 12, 18, 31, 31, 37, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 32) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]1(CC)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721154810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721154810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721154810 none CCN(CCNC(=O)[C@@]1(CC)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 12, 18, 33, 33, 38, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 18, 18, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721154810 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154810 Building ZINC001721154811 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721154811 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/33 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]1(CC)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721154811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721154811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721154811 none CCN(CCNC(=O)[C@]1(CC)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 12, 18, 34, 34, 38, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 18, 18, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/34 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]1(CC)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721154811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721154811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721154811 none CCN(CCNC(=O)[C@]1(CC)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 12, 18, 29, 29, 38, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 18, 18, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721154811 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 Building ZINC001721154811 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721154811 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 33) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]1(CC)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721154811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721154811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721154811 none CCN(CCNC(=O)[C@]1(CC)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 12, 18, 34, 34, 38, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 18, 18, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 34) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]1(CC)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721154811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721154811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721154811 none CCN(CCNC(=O)[C@]1(CC)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 12, 18, 29, 29, 38, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 18, 18, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721154811 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721154811 Building ZINC001721155972 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721155972 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/35 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721155972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721155972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721155972 none CCN(CCNC(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 12, 16, 22, 22, 33, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 16, 16, 22, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/36 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721155972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721155972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721155972 none CCN(CCNC(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 11, 15, 26, 26, 35, 49, 49, 49, 49, 49, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 15, 15, 26, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721155972 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 Building ZINC001721155972 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721155972 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 35) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721155972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721155972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721155972 none CCN(CCNC(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 12, 16, 22, 22, 33, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 16, 16, 22, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 36) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721155972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721155972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721155972 none CCN(CCNC(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 11, 15, 26, 26, 35, 49, 49, 49, 49, 49, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 15, 15, 26, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721155972 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155972 Building ZINC001721155973 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721155973 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/37 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721155973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721155973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721155973 none CCN(CCNC(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 11, 15, 26, 26, 28, 49, 49, 49, 49, 49, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 15, 15, 26, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/38 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721155973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721155973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721155973 none CCN(CCNC(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 2, 4, 11, 15, 24, 24, 25, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 15, 15, 24, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721155973 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 Building ZINC001721155973 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721155973 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 37) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721155973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721155973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721155973 none CCN(CCNC(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 11, 15, 26, 26, 28, 49, 49, 49, 49, 49, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 15, 15, 26, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 38) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721155973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721155973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721155973 none CCN(CCNC(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 2, 4, 11, 15, 24, 24, 25, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 15, 15, 24, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721155973 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721155973 Building ZINC001721156373 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721156373 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/39 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCN1C(N)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721156373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721156373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721156373 none CCN(CCNC(=O)[C@@H]1CCCN1C(N)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 9, 10, 16, 16, 21, 43, 43, 43, 43, 43, 43, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 10, 10, 16, 43, 43, 43, 43, 43, 43, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/40 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCN1C(N)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721156373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721156373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721156373 none CCN(CCNC(=O)[C@@H]1CCCN1C(N)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 9, 9, 19, 19, 20, 39, 39, 39, 39, 39, 39, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 19, 39, 39, 39, 39, 39, 39, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 174 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721156373 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 Building ZINC001721156373 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721156373 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 39) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCN1C(N)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721156373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721156373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721156373 none CCN(CCNC(=O)[C@@H]1CCCN1C(N)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 9, 10, 16, 16, 21, 43, 43, 43, 43, 43, 43, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 10, 10, 16, 43, 43, 43, 43, 43, 43, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 40) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCN1C(N)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721156373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721156373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721156373 none CCN(CCNC(=O)[C@@H]1CCCN1C(N)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 9, 9, 19, 19, 20, 39, 39, 39, 39, 39, 39, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 19, 39, 39, 39, 39, 39, 39, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 174 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721156373 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156373 Building ZINC001721156992 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721156992 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/41 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cc(C(N)=O)ccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721156992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721156992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721156992 none CCN(CCNC(=O)c1cc(C(N)=O)ccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 9, 14, 36, 36, 36, 39, 39, 39, 46, 46, 39, 39, 39, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 14, 14, 36, 39, 46, 46, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/42 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cc(C(N)=O)ccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721156992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721156992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721156992 none CCN(CCNC(=O)c1cc(C(N)=O)ccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 9, 15, 38, 38, 38, 40, 40, 40, 47, 47, 40, 40, 40, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 15, 15, 38, 40, 47, 47, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721156992 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 Building ZINC001721156992 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721156992 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 41) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cc(C(N)=O)ccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721156992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721156992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721156992 none CCN(CCNC(=O)c1cc(C(N)=O)ccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 9, 14, 36, 36, 36, 39, 39, 39, 46, 46, 39, 39, 39, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 14, 14, 36, 39, 46, 46, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 42) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cc(C(N)=O)ccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721156992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721156992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721156992 none CCN(CCNC(=O)c1cc(C(N)=O)ccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 9, 15, 38, 38, 38, 40, 40, 40, 47, 47, 40, 40, 40, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 15, 15, 38, 40, 47, 47, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721156992 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721156992 Building ZINC001721158294 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721158294 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/43 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cn2cccnc2n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721158294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721158294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721158294 none CCN(CCNC(=O)c1cn2cccnc2n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 7, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 14, 14, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/44 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cn2cccnc2n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721158294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721158294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721158294 none CCN(CCNC(=O)c1cn2cccnc2n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 7, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 14, 14, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721158294 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 Building ZINC001721158294 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721158294 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 43) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cn2cccnc2n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721158294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721158294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721158294 none CCN(CCNC(=O)c1cn2cccnc2n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 7, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 14, 14, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 44) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)c1cn2cccnc2n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721158294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721158294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721158294 none CCN(CCNC(=O)c1cn2cccnc2n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 7, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 14, 14, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721158294 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721158294 Building ZINC001721166913 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721166913 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/45 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCc2nn[nH]c21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721166913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721166913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721166913 none CCN(CCNC(=O)[C@@H]1CCCc2nn[nH]c21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 11, 15, 30, 30, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 15, 15, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/46 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCc2nn[nH]c21)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721166913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721166913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721166913 none CCN(CCNC(=O)[C@@H]1CCCc2nn[nH]c21)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 11, 13, 28, 28, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 13, 13, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721166913 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 Building ZINC001721166913 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721166913 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 45) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCc2nn[nH]c21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721166913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721166913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721166913 none CCN(CCNC(=O)[C@@H]1CCCc2nn[nH]c21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 11, 15, 30, 30, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 15, 15, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 46) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@H]1CCCc2nn[nH]c21)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721166913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721166913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721166913 none CCN(CCNC(=O)[C@@H]1CCCc2nn[nH]c21)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 11, 13, 28, 28, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 13, 13, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721166913 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166913 Building ZINC001721166914 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721166914 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/47 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CCCc2nn[nH]c21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721166914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721166914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721166914 none CCN(CCNC(=O)[C@H]1CCCc2nn[nH]c21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 11, 13, 28, 28, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 13, 13, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/48 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CCCc2nn[nH]c21)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721166914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721166914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721166914 none CCN(CCNC(=O)[C@H]1CCCc2nn[nH]c21)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 11, 15, 30, 30, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 15, 15, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721166914 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 Building ZINC001721166914 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721166914 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 47) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CCCc2nn[nH]c21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721166914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721166914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721166914 none CCN(CCNC(=O)[C@H]1CCCc2nn[nH]c21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 11, 13, 28, 28, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 13, 13, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 48) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@H]1CCCc2nn[nH]c21)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721166914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721166914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721166914 none CCN(CCNC(=O)[C@H]1CCCc2nn[nH]c21)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 11, 15, 30, 30, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 15, 15, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721166914 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721166914 Building ZINC001721180641 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180641 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/49 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)c1cncnc1O) `ZINC001721180641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721180641 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 28, 28, 28, 28, 28, 28, 38, 38, 50, 50, 38, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 28, 28, 28, 28, 28, 28, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 304 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/50 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)c1cncnc1O) `ZINC001721180641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721180641 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 32, 32, 32, 32, 32, 32, 41, 41, 50, 50, 41, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 32, 32, 32, 32, 32, 32, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 294 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180641 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 Building ZINC001721180641 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180641 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 49) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)c1cncnc1O) `ZINC001721180641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721180641 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 28, 28, 28, 28, 28, 28, 38, 38, 50, 50, 38, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 28, 28, 28, 28, 28, 28, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 304 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 50) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)c1cncnc1O) `ZINC001721180641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721180641 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 32, 32, 32, 32, 32, 32, 41, 41, 50, 50, 41, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 32, 32, 32, 32, 32, 32, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 294 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180641 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180641 Building ZINC001721180668 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180668 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/51 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cncn1) `ZINC001721180668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180668 none C[C@H](C(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 38, 45, 28, 38, 28, 28, 28, 28, 19, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50, 50, 45, 45, 45, 28, 28, 28, 28, 28, 28, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/52 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cncn1) `ZINC001721180668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180668 none C[C@H](C(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 37, 45, 26, 37, 26, 26, 26, 26, 18, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50, 50, 45, 45, 45, 26, 26, 26, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180668 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 Building ZINC001721180668 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180668 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 51) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cncn1) `ZINC001721180668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180668 none C[C@H](C(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 38, 45, 28, 38, 28, 28, 28, 28, 19, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50, 50, 45, 45, 45, 28, 28, 28, 28, 28, 28, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 52) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cncn1) `ZINC001721180668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180668 none C[C@H](C(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 37, 45, 26, 37, 26, 26, 26, 26, 18, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50, 50, 45, 45, 45, 26, 26, 26, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180668 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180668 Building ZINC001721180669 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180669 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/53 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cncn1) `ZINC001721180669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180669 none C[C@@H](C(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 46, 30, 35, 30, 30, 30, 30, 17, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 46, 46, 46, 30, 30, 30, 30, 30, 30, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 171 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/54 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cncn1) `ZINC001721180669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180669 none C[C@@H](C(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 33, 48, 26, 33, 26, 26, 26, 26, 16, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 48, 48, 48, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180669 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 Building ZINC001721180669 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180669 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 53) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cncn1) `ZINC001721180669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180669 none C[C@@H](C(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 46, 30, 35, 30, 30, 30, 30, 17, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 46, 46, 46, 30, 30, 30, 30, 30, 30, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 171 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 54) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cncn1) `ZINC001721180669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180669 none C[C@@H](C(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 33, 48, 26, 33, 26, 26, 26, 26, 16, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 48, 48, 48, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180669 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180669 Building ZINC001721180739 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180739 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/55 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CC1OCCCO1) `ZINC001721180739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721180739 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 26, 26, 26, 26, 26, 26, 30, 30, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 26, 26, 26, 26, 26, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/56 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CC1OCCCO1) `ZINC001721180739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721180739 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 25, 25, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 22, 22, 22, 22, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180739 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 Building ZINC001721180739 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180739 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 55) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CC1OCCCO1) `ZINC001721180739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721180739 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 26, 26, 26, 26, 26, 26, 30, 30, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 26, 26, 26, 26, 26, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 56) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CC1OCCCO1) `ZINC001721180739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721180739 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 25, 25, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 22, 22, 22, 22, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180739 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180739 Building ZINC001721180740 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180740 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/57 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CC1OCCCO1) `ZINC001721180740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721180740 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 24, 24, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 21, 21, 21, 21, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/58 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CC1OCCCO1) `ZINC001721180740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721180740 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 28, 28, 28, 28, 28, 28, 32, 32, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 28, 28, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180740 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 Building ZINC001721180740 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180740 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 57) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CC1OCCCO1) `ZINC001721180740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721180740 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 24, 24, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 21, 21, 21, 21, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 58) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CC1OCCCO1) `ZINC001721180740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721180740 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 28, 28, 28, 28, 28, 28, 32, 32, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 28, 28, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180740 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180740 Building ZINC001721180798 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180798 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/59 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721180798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180798 none COc1cncc(C(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 26, 38, 26, 26, 26, 26, 17, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/60 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721180798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180798 none COc1cncc(C(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 30, 41, 30, 30, 30, 30, 17, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180798 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 Building ZINC001721180798 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180798 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 59) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721180798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180798 none COc1cncc(C(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 26, 38, 26, 26, 26, 26, 17, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 60) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721180798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721180798 none COc1cncc(C(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 30, 41, 30, 30, 30, 30, 17, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180798 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180798 Building ZINC001721180952 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180952 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/61 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721180952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721180952 none Cc1nnc(CC(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 22, 20, 22, 20, 20, 20, 20, 14, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 39, 39, 20, 20, 20, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 169 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/62 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721180952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721180952 none Cc1nnc(CC(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 15, 13, 15, 13, 13, 13, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 34, 34, 13, 13, 13, 13, 13, 13, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180952 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 Building ZINC001721180952 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721180952 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 61) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721180952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721180952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721180952 none Cc1nnc(CC(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 22, 20, 22, 20, 20, 20, 20, 14, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 39, 39, 20, 20, 20, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 169 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 62) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721180952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721180952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721180952 none Cc1nnc(CC(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 15, 13, 15, 13, 13, 13, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 34, 34, 13, 13, 13, 13, 13, 13, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721180952 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721180952 Building ZINC001721181035 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721181035 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/63 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721181035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721181035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721181035 none Cc1nccn1CC(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 26, 21, 26, 21, 21, 21, 21, 15, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 45, 21, 21, 21, 21, 21, 21, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 178 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/64 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721181035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721181035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721181035 none Cc1nccn1CC(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 43, 20, 17, 20, 17, 17, 17, 17, 12, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 17, 17, 17, 17, 17, 17, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721181035 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 Building ZINC001721181035 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721181035 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 63) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721181035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721181035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721181035 none Cc1nccn1CC(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 26, 21, 26, 21, 21, 21, 21, 15, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 45, 21, 21, 21, 21, 21, 21, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 178 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 64) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721181035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721181035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721181035 none Cc1nccn1CC(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 43, 20, 17, 20, 17, 17, 17, 17, 12, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 17, 17, 17, 17, 17, 17, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721181035 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181035 Building ZINC001721181497 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721181497 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/65 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CCS(C)(=O)=O) `ZINC001721181497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721181497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721181497 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 30, 30, 41, 42, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 22, 22, 22, 22, 41, 41, 42, 42, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 210 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/66 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CCS(C)(=O)=O) `ZINC001721181497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721181497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721181497 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 22, 22, 22, 22, 22, 22, 30, 30, 44, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 22, 22, 22, 22, 22, 22, 44, 44, 44, 44, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721181497 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 Building ZINC001721181497 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721181497 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 65) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CCS(C)(=O)=O) `ZINC001721181497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721181497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721181497 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 30, 30, 41, 42, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 22, 22, 22, 22, 41, 41, 42, 42, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 210 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 66) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CCS(C)(=O)=O) `ZINC001721181497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721181497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721181497 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 22, 22, 22, 22, 22, 22, 30, 30, 44, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 22, 22, 22, 22, 22, 22, 44, 44, 44, 44, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721181497 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181497 Building ZINC001721181722 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721181722 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/67 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721181722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721181722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721181722 none COCCOCCC(=O)N1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 34, 23, 23, 16, 15, 16, 15, 15, 15, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 15, 15, 15, 15, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/68 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721181722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721181722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721181722 none COCCOCCC(=O)N1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 36, 18, 18, 9, 9, 9, 9, 9, 9, 9, 6, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721181722 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 Building ZINC001721181722 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721181722 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 67) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721181722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721181722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721181722 none COCCOCCC(=O)N1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 34, 23, 23, 16, 15, 16, 15, 15, 15, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 15, 15, 15, 15, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 68) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/68: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721181722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721181722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721181722 none COCCOCCC(=O)N1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 36, 18, 18, 9, 9, 9, 9, 9, 9, 9, 6, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721181722 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181722 Building ZINC001721181723 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721181723 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/69 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721181723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721181723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721181723 none COCCOCCC(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 36, 17, 17, 8, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 49, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/70 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721181723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721181723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721181723 none COCCOCCC(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 22, 22, 15, 14, 15, 14, 14, 14, 14, 11, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 14, 14, 14, 14, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721181723 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 Building ZINC001721181723 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721181723 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 69) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/69: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721181723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721181723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721181723 none COCCOCCC(=O)N1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 36, 17, 17, 8, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 49, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 70) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721181723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721181723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721181723 none COCCOCCC(=O)N1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 22, 22, 15, 14, 15, 14, 14, 14, 14, 11, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 14, 14, 14, 14, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721181723 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181723 Building ZINC001721181842 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721181842 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/71 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721181842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721181842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721181842 none Cc1c(CC(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 24, 22, 24, 22, 22, 22, 22, 15, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 47, 22, 22, 22, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/72 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721181842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721181842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721181842 none Cc1c(CC(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 26, 20, 26, 20, 20, 20, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 44, 44, 20, 20, 20, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721181842 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 Building ZINC001721181842 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721181842 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 71) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721181842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721181842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721181842 none Cc1c(CC(=O)N2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 24, 22, 24, 22, 22, 22, 22, 15, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 47, 22, 22, 22, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 72) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721181842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721181842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721181842 none Cc1c(CC(=O)N2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 26, 20, 26, 20, 20, 20, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 44, 44, 20, 20, 20, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721181842 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721181842 Building ZINC001721183814 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721183814 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/73 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CC1OCCCO1) `ZINC001721183814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721183814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721183814 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 24, 24, 24, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 12, 12, 24, 49, 49, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/74 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CC1OCCCO1) `ZINC001721183814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721183814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721183814 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 14, 26, 26, 26, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 26, 49, 49, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721183814 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 Building ZINC001721183814 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721183814 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 73) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CC1OCCCO1) `ZINC001721183814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721183814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721183814 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 24, 24, 24, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 12, 12, 24, 49, 49, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 74) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CC1OCCCO1) `ZINC001721183814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721183814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721183814 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 14, 26, 26, 26, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 26, 49, 49, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721183814 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721183814 Building ZINC001721184286 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721184286 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/75 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)NC[C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721184286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721184286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721184286 none Cc1nnc(CC(=O)NC[C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 29, 29, 29, 13, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 29, 13, 13, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/76 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)NC[C@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721184286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721184286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721184286 none Cc1nnc(CC(=O)NC[C@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 27, 27, 27, 15, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 27, 15, 15, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721184286 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 Building ZINC001721184286 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721184286 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 75) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)NC[C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721184286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721184286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721184286 none Cc1nnc(CC(=O)NC[C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 29, 29, 29, 13, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 29, 13, 13, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 76) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)NC[C@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721184286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721184286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721184286 none Cc1nnc(CC(=O)NC[C@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 27, 27, 27, 15, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 27, 15, 15, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721184286 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184286 Building ZINC001721184287 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721184287 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/77 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)NC[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721184287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721184287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721184287 none Cc1nnc(CC(=O)NC[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 24, 24, 24, 13, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 24, 13, 13, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/78 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)NC[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721184287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721184287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721184287 none Cc1nnc(CC(=O)NC[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 25, 25, 25, 11, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 25, 11, 11, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721184287 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 Building ZINC001721184287 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721184287 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 77) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)NC[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721184287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721184287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721184287 none Cc1nnc(CC(=O)NC[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 24, 24, 24, 13, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 24, 13, 13, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 78) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)NC[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001721184287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721184287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721184287 none Cc1nnc(CC(=O)NC[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 25, 25, 25, 11, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 25, 11, 11, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721184287 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721184287 Building ZINC001721190486 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721190486 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/79 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)NC[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721190486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721190486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721190486 none Cc1c(CC(=O)NC[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 24, 24, 24, 12, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 24, 12, 12, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/80 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)NC[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721190486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721190486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721190486 none Cc1c(CC(=O)NC[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 15, 15, 15, 8, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 35, 35, 15, 8, 8, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721190486 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 Building ZINC001721190486 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721190486 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 79) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)NC[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721190486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721190486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721190486 none Cc1c(CC(=O)NC[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 24, 24, 24, 12, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 24, 12, 12, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 80) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)NC[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721190486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721190486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721190486 none Cc1c(CC(=O)NC[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 15, 15, 15, 8, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 35, 35, 15, 8, 8, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721190486 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721190486 Building ZINC001721200397 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721200397 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/81 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CCCCC(N)=O) `ZINC001721200397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721200397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721200397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CCCCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 4, 7, 7, 7, 21, 24, 34, 47, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 4, 7, 21, 21, 29, 29, 32, 33, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/82 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CCCCC(N)=O) `ZINC001721200397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721200397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721200397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CCCCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 20, 29, 34, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 7, 20, 20, 33, 33, 33, 33, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721200397 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 Building ZINC001721200397 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721200397 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 81) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CCCCC(N)=O) `ZINC001721200397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721200397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721200397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CCCCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 4, 7, 7, 7, 21, 24, 34, 47, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 4, 7, 21, 21, 29, 29, 32, 33, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 82) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CCCCC(N)=O) `ZINC001721200397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721200397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721200397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CNC(=O)CCCCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 20, 29, 34, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 7, 20, 20, 33, 33, 33, 33, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721200397 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721200397 Building ZINC001721205123 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205123 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/83 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721205123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205123 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 24, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 29, 29, 35, 35, 35, 35, 35, 44, 44, 32, 32, 32, 32, 32, 32, 32, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 44, 44] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 224 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/84 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721205123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205123 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 24, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 27, 27, 36, 36, 36, 36, 36, 46, 46, 35, 35, 35, 35, 35, 34, 34, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 46, 46] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 247 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205123 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 Building ZINC001721205123 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205123 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 83) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721205123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205123 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 24, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 29, 29, 35, 35, 35, 35, 35, 44, 44, 32, 32, 32, 32, 32, 32, 32, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 44, 44] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 224 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 84) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721205123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205123 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 24, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 27, 27, 36, 36, 36, 36, 36, 46, 46, 35, 35, 35, 35, 35, 34, 34, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 46, 46] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 247 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205123 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205123 Building ZINC001721205147 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205147 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/85 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1N) `ZINC001721205147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721205147 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 22, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 38, 38, 49, 49, 49, 49, 49, 49, 31, 31, 31, 31, 31, 29, 29, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/86 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1N) `ZINC001721205147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721205147 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 38, 38, 48, 48, 48, 48, 48, 48, 31, 31, 31, 31, 31, 29, 29, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205147 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 Building ZINC001721205147 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205147 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 85) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1N) `ZINC001721205147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721205147 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 22, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 38, 38, 49, 49, 49, 49, 49, 49, 31, 31, 31, 31, 31, 29, 29, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 86) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1N) `ZINC001721205147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721205147 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn(C)c1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 38, 38, 48, 48, 48, 48, 48, 48, 31, 31, 31, 31, 31, 29, 29, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205147 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205147 Building ZINC001721205189 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205189 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/87 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)ccc1=O) `ZINC001721205189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721205189 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 36, 30, 20, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 36, 36, 44, 44, 44, 44, 44, 44, 44, 39, 39, 39, 39, 39, 37, 37, 20, 20, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/88 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)ccc1=O) `ZINC001721205189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721205189 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 29, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 37, 37, 45, 45, 45, 45, 45, 45, 45, 37, 37, 37, 37, 37, 35, 35, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205189 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 Building ZINC001721205189 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205189 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 87) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)ccc1=O) `ZINC001721205189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721205189 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 36, 30, 20, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 36, 36, 44, 44, 44, 44, 44, 44, 44, 39, 39, 39, 39, 39, 37, 37, 20, 20, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 88) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)ccc1=O) `ZINC001721205189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721205189 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 29, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 37, 37, 45, 45, 45, 45, 45, 45, 45, 37, 37, 37, 37, 37, 35, 35, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205189 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205189 Building ZINC001721205194 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205194 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/89 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1) `ZINC001721205194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721205194 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 19, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 28, 36, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 27, 27, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/90 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1) `ZINC001721205194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721205194 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 20, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 29, 36, 44, 44, 44, 44, 44, 28, 28, 28, 28, 28, 28, 28, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205194 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 Building ZINC001721205194 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205194 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 89) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1) `ZINC001721205194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721205194 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 19, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 28, 36, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 27, 27, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 90) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1) `ZINC001721205194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721205194 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 20, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 29, 36, 44, 44, 44, 44, 44, 28, 28, 28, 28, 28, 28, 28, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205194 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205194 Building ZINC001721205214 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205214 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/91 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nc[nH]n1) `ZINC001721205214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721205214 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 13, 10, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 15, 15, 16, 16, 44, 44, 44, 44, 44, 16, 16, 16, 16, 16, 16, 16, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 44] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/92 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nc[nH]n1) `ZINC001721205214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721205214 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 14, 14, 15, 15, 44, 44, 44, 44, 44, 15, 15, 15, 15, 15, 15, 15, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 44] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205214 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 Building ZINC001721205214 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205214 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 91) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nc[nH]n1) `ZINC001721205214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721205214 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 13, 10, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 15, 15, 16, 16, 44, 44, 44, 44, 44, 16, 16, 16, 16, 16, 16, 16, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 44] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 92) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nc[nH]n1) `ZINC001721205214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721205214 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 14, 14, 15, 15, 44, 44, 44, 44, 44, 15, 15, 15, 15, 15, 15, 15, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 44] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205214 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205214 Building ZINC001721205228 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205228 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/93 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1nonc1C) `ZINC001721205228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205228 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1nonc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 8, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 27, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 32, 32, 38, 44, 44, 44, 44, 44, 33, 33, 33, 33, 33, 33, 33, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/94 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1nonc1C) `ZINC001721205228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205228 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1nonc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 8, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 26, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 31, 31, 38, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 32, 32, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205228 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 Building ZINC001721205228 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205228 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 93) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1nonc1C) `ZINC001721205228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205228 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1nonc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 8, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 27, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 32, 32, 38, 44, 44, 44, 44, 44, 33, 33, 33, 33, 33, 33, 33, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 94) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1nonc1C) `ZINC001721205228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205228 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1nonc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 8, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 26, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 31, 31, 38, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 32, 32, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205228 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205228 Building ZINC001721205330 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205330 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/95 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncnc1O) `ZINC001721205330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721205330 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 32, 26, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 42, 42, 50, 50, 48, 50, 50, 50, 34, 34, 34, 34, 34, 32, 32, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 100] 100 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 321 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/96 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncnc1O) `ZINC001721205330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721205330 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [30, 28, 25, 14, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 38, 38, 48, 48, 47, 48, 48, 48, 30, 30, 30, 30, 30, 28, 28, 14, 14, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 96] 100 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205330 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 Building ZINC001721205330 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205330 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 95) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncnc1O) `ZINC001721205330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721205330 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 32, 26, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 42, 42, 50, 50, 48, 50, 50, 50, 34, 34, 34, 34, 34, 32, 32, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 100] 100 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 321 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 96) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncnc1O) `ZINC001721205330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721205330 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [30, 28, 25, 14, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 38, 38, 48, 48, 47, 48, 48, 48, 30, 30, 30, 30, 30, 28, 28, 14, 14, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 96] 100 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205330 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205330 Building ZINC001721205494 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205494 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/97 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1) `ZINC001721205494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205494 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 28, 22, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 35, 35, 45, 45, 45, 45, 45, 45, 30, 30, 30, 30, 30, 29, 29, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 135] 150 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/98 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1) `ZINC001721205494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205494 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 28, 22, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 34, 34, 45, 45, 45, 45, 45, 45, 30, 30, 30, 30, 30, 29, 29, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 135] 150 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205494 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 Building ZINC001721205494 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205494 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 97) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1) `ZINC001721205494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205494 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 28, 22, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 35, 35, 45, 45, 45, 45, 45, 45, 30, 30, 30, 30, 30, 29, 29, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 135] 150 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 98) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1) `ZINC001721205494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721205494 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 28, 22, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 34, 34, 45, 45, 45, 45, 45, 45, 30, 30, 30, 30, 30, 29, 29, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 135] 150 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205494 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205494 Building ZINC001721205515 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205515 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/99 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCOCC1) `ZINC001721205515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721205515 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 20, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 22, 22, 34, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/100 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCOCC1) `ZINC001721205515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721205515 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 20, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 22, 22, 34, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205515 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 Building ZINC001721205515 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205515 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 99) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCOCC1) `ZINC001721205515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721205515 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 20, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 22, 22, 34, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 100) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCOCC1) `ZINC001721205515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721205515 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 20, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 22, 22, 34, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205515 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205515 Building ZINC001721205682 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205682 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/101 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccnn1C) `ZINC001721205682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721205682 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 21, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 26, 26, 37, 47, 47, 47, 47, 47, 28, 28, 28, 28, 28, 27, 27, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 47, 47, 47, 47, 47] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/102 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccnn1C) `ZINC001721205682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721205682 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 21, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 26, 26, 37, 47, 47, 47, 47, 47, 28, 28, 28, 28, 28, 27, 27, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 47, 47, 47, 47, 47] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205682 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 Building ZINC001721205682 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721205682 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 101) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccnn1C) `ZINC001721205682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721205682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721205682 none CCCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 21, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 26, 26, 37, 47, 47, 47, 47, 47, 28, 28, 28, 28, 28, 27, 27, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 47, 47, 47, 47, 47] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 102) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccnn1C) `ZINC001721205682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721205682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721205682 none CCCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 21, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 26, 26, 37, 47, 47, 47, 47, 47, 28, 28, 28, 28, 28, 27, 27, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 47, 47, 47, 47, 47] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721205682 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721205682 Building ZINC001721211053 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721211053 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/103 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)C[C@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721211053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721211053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721211053 none CCCN(CCNC(=O)C[C@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 7, 7, 8, 8, 8, 39, 49, 49, 49, 49, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 8, 39, 39, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/104 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)C[C@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721211053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721211053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721211053 none CCCN(CCNC(=O)C[C@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 7, 7, 7, 7, 7, 36, 46, 46, 46, 46, 46, 46, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 36, 36, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721211053 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 Building ZINC001721211053 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721211053 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 103) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)C[C@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721211053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721211053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721211053 none CCCN(CCNC(=O)C[C@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 7, 7, 8, 8, 8, 39, 49, 49, 49, 49, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 8, 39, 39, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 104) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)C[C@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721211053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721211053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721211053 none CCCN(CCNC(=O)C[C@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 7, 7, 7, 7, 7, 36, 46, 46, 46, 46, 46, 46, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 36, 36, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721211053 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211053 Building ZINC001721211054 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721211054 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/105 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)C[C@@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721211054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721211054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721211054 none CCCN(CCNC(=O)C[C@@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 2, 3, 7, 7, 8, 8, 8, 40, 49, 49, 49, 49, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 8, 40, 40, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/106 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)C[C@@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721211054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721211054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721211054 none CCCN(CCNC(=O)C[C@@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 7, 7, 8, 8, 8, 39, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 8, 39, 39, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721211054 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 Building ZINC001721211054 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721211054 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 105) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)C[C@@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721211054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721211054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721211054 none CCCN(CCNC(=O)C[C@@H]1CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 2, 3, 7, 7, 8, 8, 8, 40, 49, 49, 49, 49, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 8, 40, 40, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 106) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)C[C@@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721211054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721211054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721211054 none CCCN(CCNC(=O)C[C@@H]1CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 7, 7, 8, 8, 8, 39, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 8, 39, 39, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721211054 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721211054 Building ZINC001721219141 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721219141 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/107 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)c1cccc(=O)n1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721219141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721219141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721219141 none CCCN(CCNC(=O)c1cccc(=O)n1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 6, 3, 6, 13, 17, 31, 31, 31, 45, 45, 45, 45, 45, 45, 45, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 13, 13, 13, 13, 17, 17, 31, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/108 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)c1cccc(=O)n1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721219141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721219141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721219141 none CCCN(CCNC(=O)c1cccc(=O)n1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 7, 3, 7, 16, 20, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 1, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 14, 14, 16, 16, 20, 20, 30, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 188 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721219141 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 Building ZINC001721219141 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721219141 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 107) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)c1cccc(=O)n1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721219141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721219141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721219141 none CCCN(CCNC(=O)c1cccc(=O)n1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 6, 3, 6, 13, 17, 31, 31, 31, 45, 45, 45, 45, 45, 45, 45, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 13, 13, 13, 13, 17, 17, 31, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 108) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)c1cccc(=O)n1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721219141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721219141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721219141 none CCCN(CCNC(=O)c1cccc(=O)n1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 7, 3, 7, 16, 20, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 1, 3, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 14, 14, 16, 16, 20, 20, 30, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 188 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721219141 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721219141 Building ZINC001721224818 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721224818 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/109 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721224818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721224818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721224818 none CC[C@@H](NC(C)=O)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 32, 44, 44, 50, 50, 50, 25, 32, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 271 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/110 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721224818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721224818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721224818 none CC[C@@H](NC(C)=O)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 41, 29, 41, 41, 50, 50, 50, 22, 29, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 291 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721224818 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 Building ZINC001721224818 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721224818 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 109) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721224818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721224818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721224818 none CC[C@@H](NC(C)=O)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 32, 44, 44, 50, 50, 50, 25, 32, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 271 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 110) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721224818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721224818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721224818 none CC[C@@H](NC(C)=O)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 41, 29, 41, 41, 50, 50, 50, 22, 29, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 291 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721224818 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224818 Building ZINC001721224821 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721224821 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/111 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721224821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721224821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721224821 none CC[C@H](NC(C)=O)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 39, 26, 39, 39, 50, 50, 50, 19, 26, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 27, 27, 49, 49, 49, 49, 49, 50, 50, 50, 50, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 318 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/112 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721224821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721224821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721224821 none CC[C@H](NC(C)=O)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 38, 28, 38, 38, 50, 50, 50, 20, 28, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 330 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721224821 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 Building ZINC001721224821 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721224821 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 111) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721224821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721224821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721224821 none CC[C@H](NC(C)=O)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 39, 26, 39, 39, 50, 50, 50, 19, 26, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 27, 27, 49, 49, 49, 49, 49, 50, 50, 50, 50, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 318 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 112) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721224821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721224821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721224821 none CC[C@H](NC(C)=O)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 38, 28, 38, 38, 50, 50, 50, 20, 28, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 330 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721224821 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224821 Building ZINC001721224913 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721224913 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/113 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnn1)C1CC1) `ZINC001721224913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721224913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721224913 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 11, 24, 27, 27, 41, 43, 50, 50, 50, 50, 24, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 41, 41, 43, 43, 50, 50, 26, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/114 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnn1)C1CC1) `ZINC001721224913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721224913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721224913 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 26, 27, 27, 37, 41, 50, 50, 50, 50, 26, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 37, 37, 41, 41, 50, 50, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721224913 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 Building ZINC001721224913 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721224913 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 113) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnn1)C1CC1) `ZINC001721224913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721224913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721224913 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 11, 24, 27, 27, 41, 43, 50, 50, 50, 50, 24, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 41, 41, 43, 43, 50, 50, 26, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 114) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnn1)C1CC1) `ZINC001721224913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721224913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721224913 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 26, 27, 27, 37, 41, 50, 50, 50, 50, 26, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 37, 37, 41, 41, 50, 50, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721224913 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224913 Building ZINC001721224948 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721224948 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/115 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721224948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721224948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721224948 none COc1ccc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 35, 45, 17, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 37, 37, 50, 50, 50, 50, 50, 50, 50, 17, 17, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/116 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721224948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721224948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721224948 none COc1ccc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 33, 40, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 38, 38, 50, 50, 50, 50, 50, 50, 50, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721224948 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 Building ZINC001721224948 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721224948 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 115) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721224948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721224948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721224948 none COc1ccc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 35, 45, 17, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 37, 37, 50, 50, 50, 50, 50, 50, 50, 17, 17, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 116) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721224948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721224948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721224948 none COc1ccc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 33, 40, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 38, 38, 50, 50, 50, 50, 50, 50, 50, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721224948 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721224948 Building ZINC001721225008 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225008 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/117 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O) `ZINC001721225008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225008 none C[C@@H](C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 33, 44, 27, 33, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 35, 35, 44, 49, 49, 49, 44, 44, 44, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 250 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/118 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O) `ZINC001721225008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225008 none C[C@@H](C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 34, 43, 28, 34, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 34, 34, 43, 50, 50, 50, 43, 43, 43, 15, 15, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 243 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225008 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 Building ZINC001721225008 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225008 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 117) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O) `ZINC001721225008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225008 none C[C@@H](C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 33, 44, 27, 33, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 35, 35, 44, 49, 49, 49, 44, 44, 44, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 250 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 118) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O) `ZINC001721225008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225008 none C[C@@H](C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 34, 43, 28, 34, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 34, 34, 43, 50, 50, 50, 43, 43, 43, 15, 15, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 243 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225008 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225008 Building ZINC001721225009 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225009 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/119 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O) `ZINC001721225009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225009 none C[C@H](C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 36, 43, 28, 36, 17, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 36, 36, 43, 48, 48, 48, 43, 43, 43, 17, 17, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 48, 48, 48] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/120 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O) `ZINC001721225009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225009 none C[C@H](C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 31, 44, 24, 31, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 31, 31, 44, 49, 49, 49, 44, 44, 44, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 249 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225009 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 Building ZINC001721225009 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225009 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 119) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O) `ZINC001721225009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225009 none C[C@H](C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 36, 43, 28, 36, 17, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 36, 36, 43, 48, 48, 48, 43, 43, 43, 17, 17, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 48, 48, 48] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 120) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O) `ZINC001721225009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225009 none C[C@H](C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 31, 44, 24, 31, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 31, 31, 44, 49, 49, 49, 44, 44, 44, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 249 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225009 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225009 Building ZINC001721225223 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225223 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/121 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001721225223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225223 none COc1cc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 33, 44, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 37, 37, 50, 50, 50, 50, 50, 50, 50, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/122 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001721225223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225223 none COc1cc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 27, 38, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 32, 32, 50, 50, 50, 50, 50, 50, 50, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225223 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 Building ZINC001721225223 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225223 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 121) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001721225223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225223 none COc1cc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 33, 44, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 37, 37, 50, 50, 50, 50, 50, 50, 50, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 122) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001721225223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721225223 none COc1cc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 27, 38, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 32, 32, 50, 50, 50, 50, 50, 50, 50, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225223 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225223 Building ZINC001721225261 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225261 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/123 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001721225261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721225261 none Cc1cc(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 28, 20, 28, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 50, 50, 50, 50, 50, 50, 50, 47, 47, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 226 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/124 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001721225261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721225261 none Cc1cc(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 29, 24, 29, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 25, 25, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225261 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 Building ZINC001721225261 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225261 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 123) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001721225261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721225261 none Cc1cc(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 28, 20, 28, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 50, 50, 50, 50, 50, 50, 50, 47, 47, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 226 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 124) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001721225261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721225261 none Cc1cc(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 29, 24, 29, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 25, 25, 50, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225261 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225261 Building ZINC001721225278 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225278 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/125 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnc1)C1CC1) `ZINC001721225278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721225278 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 20, 21, 21, 31, 31, 50, 50, 50, 50, 20, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 11, 11, 31, 31, 31, 31, 50, 50, 50, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/126 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnc1)C1CC1) `ZINC001721225278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721225278 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 18, 19, 19, 27, 28, 50, 50, 50, 50, 18, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 11, 11, 27, 27, 28, 28, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225278 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 Building ZINC001721225278 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225278 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 125) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnc1)C1CC1) `ZINC001721225278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721225278 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 20, 21, 21, 31, 31, 50, 50, 50, 50, 20, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 11, 11, 31, 31, 31, 31, 50, 50, 50, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 126) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnc1)C1CC1) `ZINC001721225278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721225278 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1ccnc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 18, 19, 19, 27, 28, 50, 50, 50, 50, 18, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 11, 11, 27, 27, 28, 28, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225278 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225278 Building ZINC001721225569 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225569 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/127 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cnn1C) `ZINC001721225569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721225569 none Cc1c(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 24, 20, 24, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 22, 22, 50, 50, 50, 50, 50, 50, 50, 43, 43, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/128 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cnn1C) `ZINC001721225569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721225569 none Cc1c(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 24, 19, 24, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 20, 20, 50, 50, 50, 50, 50, 50, 50, 44, 44, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225569 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 Building ZINC001721225569 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225569 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 127) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cnn1C) `ZINC001721225569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721225569 none Cc1c(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 24, 20, 24, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 22, 22, 50, 50, 50, 50, 50, 50, 50, 43, 43, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 128) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cnn1C) `ZINC001721225569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721225569 none Cc1c(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 24, 19, 24, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 20, 20, 50, 50, 50, 50, 50, 50, 50, 44, 44, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225569 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225569 Building ZINC001721225806 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225806 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/129 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721225806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721225806 none Cc1ccn(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 22, 19, 22, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 22, 22, 50, 50, 50, 50, 50, 50, 47, 47, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/130 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721225806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721225806 none Cc1ccn(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 21, 17, 21, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 19, 19, 50, 50, 50, 50, 50, 50, 46, 46, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225806 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 Building ZINC001721225806 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225806 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 129) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721225806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721225806 none Cc1ccn(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 22, 19, 22, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 22, 22, 50, 50, 50, 50, 50, 50, 47, 47, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 130) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721225806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721225806 none Cc1ccn(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 21, 17, 21, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 19, 19, 50, 50, 50, 50, 50, 50, 46, 46, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225806 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225806 Building ZINC001721225836 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225836 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/131 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)c1nccnc1N)C1CC1) `ZINC001721225836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721225836 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)c1nccnc1N)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 31, 46, 46, 50, 50, 50, 50, 50, 50, 31, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 50, 50, 50, 50, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/132 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)c1nccnc1N)C1CC1) `ZINC001721225836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721225836 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)c1nccnc1N)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 30, 46, 46, 50, 50, 50, 50, 50, 50, 30, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 17, 50, 50, 50, 50, 34, 34, 34, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225836 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 Building ZINC001721225836 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721225836 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 131) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)c1nccnc1N)C1CC1) `ZINC001721225836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721225836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721225836 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)c1nccnc1N)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 31, 46, 46, 50, 50, 50, 50, 50, 50, 31, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 50, 50, 50, 50, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 132) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)c1nccnc1N)C1CC1) `ZINC001721225836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721225836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721225836 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)c1nccnc1N)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 30, 46, 46, 50, 50, 50, 50, 50, 50, 30, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 17, 50, 50, 50, 50, 34, 34, 34, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721225836 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721225836 Building ZINC001721226185 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721226185 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/133 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001721226185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721226185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721226185 none Cc1cnn(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 22, 19, 22, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 22, 22, 50, 50, 50, 50, 50, 46, 46, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/134 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001721226185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721226185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721226185 none Cc1cnn(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 21, 16, 21, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 19, 19, 50, 50, 50, 50, 50, 47, 47, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721226185 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 Building ZINC001721226185 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721226185 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 133) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001721226185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721226185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721226185 none Cc1cnn(CC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 22, 19, 22, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 22, 22, 50, 50, 50, 50, 50, 46, 46, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 134) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001721226185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721226185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721226185 none Cc1cnn(CC(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 21, 16, 21, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 19, 19, 50, 50, 50, 50, 50, 47, 47, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721226185 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226185 Building ZINC001721226396 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721226396 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/135 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721226396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721226396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721226396 none COc1cncc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 31, 42, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 35, 35, 50, 50, 50, 50, 50, 50, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/136 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/136' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721226396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721226396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721226396 none COc1cncc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 33, 42, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 36, 36, 50, 50, 50, 50, 50, 50, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721226396 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 Building ZINC001721226396 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721226396 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 135) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721226396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721226396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721226396 none COc1cncc(C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 31, 42, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 35, 35, 50, 50, 50, 50, 50, 50, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 136) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721226396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721226396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721226396 none COc1cncc(C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 33, 42, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 36, 36, 50, 50, 50, 50, 50, 50, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721226396 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226396 Building ZINC001721226414 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721226414 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/137 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)c1cnn2cc[nH]c12)C1CC1) `ZINC001721226414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721226414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721226414 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)c1cnn2cc[nH]c12)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 21, 29, 38, 38, 49, 49, 49, 49, 49, 49, 49, 49, 29, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 21, 21, 49, 49, 49, 35, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/138 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)c1cnn2cc[nH]c12)C1CC1) `ZINC001721226414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721226414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721226414 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)c1cnn2cc[nH]c12)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 20, 31, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 31, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 20, 20, 50, 50, 50, 35, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721226414 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 Building ZINC001721226414 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721226414 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 137) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)c1cnn2cc[nH]c12)C1CC1) `ZINC001721226414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721226414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721226414 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)c1cnn2cc[nH]c12)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 21, 29, 38, 38, 49, 49, 49, 49, 49, 49, 49, 49, 29, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 21, 21, 49, 49, 49, 35, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 138) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)c1cnn2cc[nH]c12)C1CC1) `ZINC001721226414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721226414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721226414 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)c1cnn2cc[nH]c12)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 20, 31, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 31, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 20, 20, 50, 50, 50, 35, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721226414 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226414 Building ZINC001721226425 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721226425 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/139 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721226425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721226425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721226425 none CC(=O)NC(C)(C)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 39, 32, 39, 39, 29, 32, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 37, 37, 49, 49, 49, 49, 39, 39, 39, 39, 39, 39, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 225 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/140 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721226425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721226425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721226425 none CC(=O)NC(C)(C)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 39, 32, 39, 39, 28, 32, 15, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 37, 37, 49, 49, 49, 49, 39, 39, 39, 39, 39, 39, 15, 15, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721226425 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 Building ZINC001721226425 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721226425 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 139) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721226425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721226425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721226425 none CC(=O)NC(C)(C)C(=O)N(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 39, 32, 39, 39, 29, 32, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 37, 37, 49, 49, 49, 49, 39, 39, 39, 39, 39, 39, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 225 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 140) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721226425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721226425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721226425 none CC(=O)NC(C)(C)C(=O)N(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 39, 32, 39, 39, 28, 32, 15, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 37, 37, 49, 49, 49, 49, 39, 39, 39, 39, 39, 39, 15, 15, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721226425 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226425 Building ZINC001721226446 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721226446 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/141 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1cccn1)C1CC1) `ZINC001721226446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721226446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721226446 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1cccn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 22, 24, 24, 36, 38, 50, 50, 50, 50, 22, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 11, 11, 36, 36, 38, 38, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/142 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1cccn1)C1CC1) `ZINC001721226446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721226446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721226446 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1cccn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 24, 25, 25, 37, 38, 50, 50, 50, 50, 24, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 37, 37, 38, 38, 50, 50, 50, 25, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721226446 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 Building ZINC001721226446 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721226446 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 141) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1cccn1)C1CC1) `ZINC001721226446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721226446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721226446 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1cccn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 22, 24, 24, 36, 38, 50, 50, 50, 50, 22, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 11, 11, 36, 36, 38, 38, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 142) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1cccn1)C1CC1) `ZINC001721226446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721226446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721226446 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)CCn1cccn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 24, 25, 25, 37, 38, 50, 50, 50, 50, 24, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 37, 37, 38, 38, 50, 50, 50, 25, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721226446 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721226446 Building ZINC001721229137 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721229137 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/143 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001721229137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721229137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721229137 none Cn1ncc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 37, 37, 26, 20, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 15, 15, 50, 50, 50, 50, 50, 50, 37, 26, 26, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/144 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001721229137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721229137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721229137 none Cn1ncc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 26, 18, 7, 4, 1, 4, 1, 1, 1, 2, 2, 2, 7, 13, 13, 50, 50, 50, 50, 50, 50, 34, 26, 26, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721229137 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 Building ZINC001721229137 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721229137 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 143) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/143: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001721229137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721229137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721229137 none Cn1ncc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 37, 37, 26, 20, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 15, 15, 50, 50, 50, 50, 50, 50, 37, 26, 26, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 144) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001721229137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721229137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721229137 none Cn1ncc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 26, 18, 7, 4, 1, 4, 1, 1, 1, 2, 2, 2, 7, 13, 13, 50, 50, 50, 50, 50, 50, 34, 26, 26, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721229137 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721229137 Building ZINC001721230643 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721230643 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/145 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721230643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721230643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721230643 none Cc1ccnn1CC(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 28, 28, 28, 24, 14, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 10, 10, 49, 49, 49, 49, 49, 49, 49, 28, 24, 24, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 250 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/146 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721230643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721230643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721230643 none Cc1ccnn1CC(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 47, 25, 25, 25, 22, 14, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 11, 11, 49, 49, 49, 49, 49, 47, 47, 25, 22, 22, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721230643 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 Building ZINC001721230643 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721230643 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 145) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721230643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721230643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721230643 none Cc1ccnn1CC(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 28, 28, 28, 24, 14, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 10, 10, 49, 49, 49, 49, 49, 49, 49, 28, 24, 24, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 250 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 146) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721230643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721230643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721230643 none Cc1ccnn1CC(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 47, 25, 25, 25, 22, 14, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 11, 11, 49, 49, 49, 49, 49, 47, 47, 25, 22, 22, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721230643 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230643 Building ZINC001721230839 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721230839 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/147 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721230839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721230839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721230839 none COc1cncc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 48, 48, 48, 28, 20, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 10, 10, 49, 49, 49, 49, 49, 49, 48, 28, 28, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/148 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721230839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721230839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721230839 none COc1cncc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 48, 48, 48, 29, 20, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 10, 10, 50, 50, 50, 50, 50, 50, 48, 29, 29, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721230839 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 Building ZINC001721230839 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721230839 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 147) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721230839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721230839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721230839 none COc1cncc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 48, 48, 48, 28, 20, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 10, 10, 49, 49, 49, 49, 49, 49, 48, 28, 28, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 148) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001721230839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721230839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721230839 none COc1cncc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 48, 48, 48, 29, 20, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 10, 10, 50, 50, 50, 50, 50, 50, 48, 29, 29, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721230839 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230839 Building ZINC001721230868 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721230868 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/149 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001721230868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721230868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721230868 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 10, 15, 16, 16, 16, 21, 45, 50, 50, 50, 50, 50, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 15, 15, 16, 21, 21, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/150 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001721230868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721230868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721230868 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 10, 16, 16, 16, 16, 22, 43, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 16, 22, 22, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721230868 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 Building ZINC001721230868 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721230868 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 149) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001721230868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721230868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721230868 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 10, 15, 16, 16, 16, 21, 45, 50, 50, 50, 50, 50, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 15, 15, 16, 21, 21, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 150) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001721230868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721230868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721230868 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 10, 16, 16, 16, 16, 22, 43, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 16, 22, 22, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721230868 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230868 Building ZINC001721230869 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721230869 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/151 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001721230869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721230869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721230869 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 10, 14, 14, 14, 14, 21, 44, 50, 50, 50, 50, 50, 4, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 14, 14, 14, 21, 21, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/152 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001721230869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721230869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721230869 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 10, 16, 17, 17, 17, 22, 45, 50, 50, 50, 50, 50, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 17, 22, 22, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721230869 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 Building ZINC001721230869 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721230869 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 151) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001721230869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721230869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721230869 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 10, 14, 14, 14, 14, 21, 44, 50, 50, 50, 50, 50, 4, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 14, 14, 14, 21, 21, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 152) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001721230869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721230869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721230869 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 10, 16, 17, 17, 17, 22, 45, 50, 50, 50, 50, 50, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 17, 22, 22, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721230869 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721230869 Building ZINC001721231760 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721231760 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/153 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1c[nH]c(C(N)=O)c1)C1CC1) `ZINC001721231760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721231760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721231760 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1c[nH]c(C(N)=O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 11, 16, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 5, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 16, 16, 22, 50, 50, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/154 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1c[nH]c(C(N)=O)c1)C1CC1) `ZINC001721231760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721231760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721231760 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1c[nH]c(C(N)=O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 12, 14, 23, 23, 23, 50, 49, 50, 50, 50, 50, 50, 50, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 14, 23, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721231760 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 Building ZINC001721231760 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721231760 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 153) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1c[nH]c(C(N)=O)c1)C1CC1) `ZINC001721231760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721231760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721231760 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1c[nH]c(C(N)=O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 11, 16, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 5, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 16, 16, 22, 50, 50, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 154) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1c[nH]c(C(N)=O)c1)C1CC1) `ZINC001721231760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721231760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721231760 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1c[nH]c(C(N)=O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 12, 14, 23, 23, 23, 50, 49, 50, 50, 50, 50, 50, 50, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 14, 23, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721231760 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721231760 Building ZINC001721232031 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721232031 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/155 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001721232031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721232031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721232031 none COc1cc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 49, 49, 28, 18, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 10, 10, 50, 50, 50, 50, 50, 50, 50, 49, 28, 28, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/156 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001721232031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721232031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721232031 none COc1cc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 49, 49, 27, 17, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 10, 10, 50, 50, 50, 50, 50, 50, 50, 49, 27, 27, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721232031 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 Building ZINC001721232031 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721232031 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 155) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001721232031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721232031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721232031 none COc1cc(C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 49, 49, 28, 18, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 10, 10, 50, 50, 50, 50, 50, 50, 50, 49, 28, 28, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 156) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001721232031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721232031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721232031 none COc1cc(C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 49, 49, 27, 17, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 10, 10, 50, 50, 50, 50, 50, 50, 50, 49, 27, 27, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721232031 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721232031 Building ZINC001721233954 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721233954 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/157 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cnnc(O)c1)C1CC1) `ZINC001721233954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721233954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721233954 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cnnc(O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 16, 17, 25, 25, 25, 49, 49, 49, 49, 49, 49, 9, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 17, 17, 25, 49, 98, 49, 13, 13, 13, 13, 13] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/158 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cnnc(O)c1)C1CC1) `ZINC001721233954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721233954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721233954 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cnnc(O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 15, 16, 26, 26, 26, 50, 50, 50, 50, 50, 50, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 16, 16, 26, 50, 100, 50, 13, 13, 13, 13, 13] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721233954 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 Building ZINC001721233954 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721233954 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 157) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cnnc(O)c1)C1CC1) `ZINC001721233954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721233954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721233954 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cnnc(O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 16, 17, 25, 25, 25, 49, 49, 49, 49, 49, 49, 9, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 17, 17, 25, 49, 98, 49, 13, 13, 13, 13, 13] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 158) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cnnc(O)c1)C1CC1) `ZINC001721233954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721233954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721233954 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cnnc(O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 15, 16, 26, 26, 26, 50, 50, 50, 50, 50, 50, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 16, 16, 26, 50, 100, 50, 13, 13, 13, 13, 13] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721233954 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721233954 Building ZINC001721234363 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721234363 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/159 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001721234363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721234363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721234363 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@H]1CCNC1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 5, 5, 11, 11, 11, 38, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 38, 38, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/160 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/160' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001721234363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721234363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721234363 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@H]1CCNC1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 13, 13, 40, 50, 50, 50, 50, 50, 50, 3, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 40, 40, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721234363 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 Building ZINC001721234363 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721234363 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 159) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001721234363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721234363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721234363 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@H]1CCNC1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 5, 5, 11, 11, 11, 38, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 38, 38, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 160) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001721234363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721234363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721234363 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@H]1CCNC1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 13, 13, 40, 50, 50, 50, 50, 50, 50, 3, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 40, 40, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721234363 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234363 Building ZINC001721234364 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721234364 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/161 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001721234364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721234364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721234364 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@@H]1CCNC1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 5, 5, 11, 11, 11, 39, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 38, 38, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/162 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001721234364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721234364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721234364 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@@H]1CCNC1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 16, 16, 16, 42, 50, 50, 50, 50, 50, 50, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 41, 41, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721234364 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 Building ZINC001721234364 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721234364 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 161) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001721234364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721234364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721234364 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@@H]1CCNC1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 5, 5, 11, 11, 11, 39, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 38, 38, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 162) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001721234364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721234364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721234364 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)C[C@@H]1CCNC1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 16, 16, 16, 42, 50, 50, 50, 50, 50, 50, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 41, 41, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721234364 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721234364 Building ZINC001721236082 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721236082 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/163 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cncnc1O)C1CC1) `ZINC001721236082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721236082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721236082 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 21, 24, 38, 38, 38, 50, 50, 38, 50, 50, 50, 11, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 24, 24, 38, 50, 50, 100, 14, 14, 14, 14, 14] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 337 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/164 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cncnc1O)C1CC1) `ZINC001721236082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721236082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721236082 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 19, 24, 39, 39, 39, 50, 50, 39, 50, 50, 50, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 24, 24, 39, 50, 50, 100, 13, 13, 13, 13, 13] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 347 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721236082 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 Building ZINC001721236082 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721236082 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 163) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cncnc1O)C1CC1) `ZINC001721236082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721236082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721236082 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 21, 24, 38, 38, 38, 50, 50, 38, 50, 50, 50, 11, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 24, 24, 38, 50, 50, 100, 14, 14, 14, 14, 14] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 337 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 164) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cncnc1O)C1CC1) `ZINC001721236082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721236082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721236082 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 19, 24, 39, 39, 39, 50, 50, 39, 50, 50, 50, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 24, 24, 39, 50, 50, 100, 13, 13, 13, 13, 13] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 347 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721236082 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721236082 Building ZINC001721238799 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721238799 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/165 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CCn1ccnc1)C1CC1) `ZINC001721238799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721238799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721238799 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CCn1ccnc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 12, 12, 12, 26, 28, 48, 48, 48, 48, 3, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 26, 26, 28, 28, 48, 48, 48, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/166 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CCn1ccnc1)C1CC1) `ZINC001721238799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721238799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721238799 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CCn1ccnc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 12, 12, 12, 27, 27, 44, 44, 44, 44, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 12, 27, 27, 27, 27, 44, 44, 44, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 21, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721238799 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 Building ZINC001721238799 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721238799 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 165) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CCn1ccnc1)C1CC1) `ZINC001721238799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721238799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721238799 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)CCn1ccnc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 12, 12, 12, 26, 28, 48, 48, 48, 48, 3, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 26, 26, 28, 28, 48, 48, 48, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 166) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CCn1ccnc1)C1CC1) `ZINC001721238799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721238799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721238799 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCNC(=O)CCn1ccnc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 12, 12, 12, 27, 27, 44, 44, 44, 44, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 12, 27, 27, 27, 27, 44, 44, 44, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 21, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721238799 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721238799 Building ZINC001721240111 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721240111 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/167 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721240111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721240111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721240111 none Cn1c(O)ncc1C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 43, 43, 29, 19, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 14, 14, 50, 50, 50, 150, 50, 43, 29, 29, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 356 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/168 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721240111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721240111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721240111 none Cn1c(O)ncc1C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 43, 43, 28, 18, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 12, 12, 50, 50, 50, 150, 50, 43, 28, 28, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 362 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721240111 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 Building ZINC001721240111 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721240111 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 167) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721240111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721240111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721240111 none Cn1c(O)ncc1C(=O)NCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 43, 43, 29, 19, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 14, 14, 50, 50, 50, 150, 50, 43, 29, 29, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 356 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 168) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721240111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721240111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721240111 none Cn1c(O)ncc1C(=O)NCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 43, 43, 28, 18, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 12, 12, 50, 50, 50, 150, 50, 43, 28, 28, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 362 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721240111 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721240111 Building ZINC001721248426 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721248426 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/169 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@H](C)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721248426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721248426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721248426 none CC(=O)NCC(=O)N[C@H](C)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 15, 15, 15, 10, 3, 10, 10, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 45, 45, 15, 10, 10, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/170 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@H](C)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721248426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721248426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721248426 none CC(=O)NCC(=O)N[C@H](C)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 12, 12, 12, 9, 3, 9, 9, 3, 3, 3, 1, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 45, 45, 12, 9, 9, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 14, 15, 48, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721248426 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 Building ZINC001721248426 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721248426 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 169) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@H](C)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721248426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721248426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721248426 none CC(=O)NCC(=O)N[C@H](C)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 15, 15, 15, 10, 3, 10, 10, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 45, 45, 15, 10, 10, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 170) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@H](C)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721248426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721248426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721248426 none CC(=O)NCC(=O)N[C@H](C)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 12, 12, 12, 9, 3, 9, 9, 3, 3, 3, 1, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 45, 45, 12, 9, 9, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 14, 15, 48, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721248426 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721248426 Building ZINC001721257387 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721257387 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/171 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnnn1C) `ZINC001721257387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721257387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721257387 none CC(C)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 23, 25, 11, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 40, 40, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/172 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnnn1C) `ZINC001721257387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721257387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721257387 none CC(C)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 26, 12, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 41, 41, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 12, 12, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721257387 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 Building ZINC001721257387 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721257387 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 171) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnnn1C) `ZINC001721257387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721257387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721257387 none CC(C)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 23, 25, 11, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 40, 40, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 172) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnnn1C) `ZINC001721257387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721257387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721257387 none CC(C)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 26, 12, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 41, 41, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 12, 12, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721257387 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721257387 Building ZINC001721278400 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278400 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/173 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278400 none CNC(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 33, 33, 33, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 32, 32, 29, 32, 32, 50, 50, 50, 50, 45, 45, 33, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 29, 32, 32] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 242 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/174 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278400 none CNC(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 34, 34, 34, 31, 14, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 34, 34, 31, 34, 34, 50, 50, 50, 50, 46, 46, 34, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 31, 34, 34] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 231 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278400 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 Building ZINC001721278400 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278400 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 173) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278400 none CNC(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 33, 33, 33, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 32, 32, 29, 32, 32, 50, 50, 50, 50, 45, 45, 33, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 29, 32, 32] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 242 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 174) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278400 none CNC(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 34, 34, 34, 31, 14, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 34, 34, 31, 34, 34, 50, 50, 50, 50, 46, 46, 34, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 31, 34, 34] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 231 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278400 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278400 Building ZINC001721278401 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278401 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/175 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278401 none CNC(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 35, 35, 35, 31, 14, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 35, 35, 31, 35, 35, 50, 50, 50, 50, 43, 43, 35, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 31, 35, 35] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 237 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/176 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278401 none CNC(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 36, 36, 36, 32, 14, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 35, 35, 32, 35, 35, 50, 50, 50, 50, 47, 47, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 32, 35, 35] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 237 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278401 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 Building ZINC001721278401 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278401 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 175) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278401 none CNC(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 35, 35, 35, 31, 14, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 35, 35, 31, 35, 35, 50, 50, 50, 50, 43, 43, 35, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 31, 35, 35] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 237 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 176) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278401 none CNC(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 36, 36, 36, 32, 14, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 35, 35, 32, 35, 35, 50, 50, 50, 50, 47, 47, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 32, 35, 35] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 237 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278401 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278401 Building ZINC001721278708 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278708 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/177 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278708.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278708 none CC(=O)NCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 36, 36, 36, 30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 35, 35, 30, 35, 35, 50, 50, 50, 50, 46, 46, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 30, 35, 35] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/178 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278708.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278708 none CC(=O)NCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 35, 35, 29, 35, 35, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 29, 35, 35] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 252 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278708 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 Building ZINC001721278708 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278708 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 177) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278708.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278708 none CC(=O)NCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 36, 36, 36, 30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 35, 35, 30, 35, 35, 50, 50, 50, 50, 46, 46, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 30, 35, 35] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 178) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278708.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278708 none CC(=O)NCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 35, 35, 29, 35, 35, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 29, 35, 35] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 252 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278708 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278708 Building ZINC001721278709 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278709 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/179 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278709 none CC(=O)NCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 35, 35, 29, 35, 35, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 29, 35, 35] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 255 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/180 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/180' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278709 none CC(=O)NCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 35, 35, 35, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 33, 33, 28, 33, 33, 50, 50, 50, 50, 46, 46, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 28, 33, 33] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 233 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278709 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 Building ZINC001721278709 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278709 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 179) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278709 none CC(=O)NCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 35, 35, 29, 35, 35, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 29, 35, 35] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 255 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 180) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721278709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721278709 none CC(=O)NCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 35, 35, 35, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 33, 33, 28, 33, 33, 50, 50, 50, 50, 46, 46, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 28, 33, 33] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 233 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278709 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278709 Building ZINC001721278868 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278868 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/181 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CC(N)=O)c1ccccc1) `ZINC001721278868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721278868 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CC(N)=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 21, 21, 21, 44, 50, 50, 18, 25, 25, 18, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 44, 44, 50, 50, 25, 25, 18, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 251 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/182 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CC(N)=O)c1ccccc1) `ZINC001721278868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721278868 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CC(N)=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 20, 20, 20, 44, 50, 50, 16, 17, 17, 16, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 44, 44, 50, 50, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 214 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278868 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 Building ZINC001721278868 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278868 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 181) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CC(N)=O)c1ccccc1) `ZINC001721278868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721278868 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CC(N)=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 21, 21, 21, 44, 50, 50, 18, 25, 25, 18, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 44, 44, 50, 50, 25, 25, 18, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 251 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 182) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CC(N)=O)c1ccccc1) `ZINC001721278868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721278868 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CC(N)=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 20, 20, 20, 44, 50, 50, 16, 17, 17, 16, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 44, 44, 50, 50, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 214 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278868 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278868 Building ZINC001721278869 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278869 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/183 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CC(N)=O)c1ccccc1) `ZINC001721278869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721278869 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CC(N)=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 20, 20, 20, 44, 50, 50, 16, 17, 17, 16, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 44, 44, 50, 50, 17, 17, 16, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 215 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/184 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CC(N)=O)c1ccccc1) `ZINC001721278869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721278869 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CC(N)=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 21, 21, 21, 44, 50, 50, 18, 24, 24, 18, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 44, 44, 50, 50, 24, 24, 18, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 243 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278869 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 Building ZINC001721278869 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721278869 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 183) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CC(N)=O)c1ccccc1) `ZINC001721278869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721278869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721278869 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CC(N)=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 20, 20, 20, 44, 50, 50, 16, 17, 17, 16, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 44, 44, 50, 50, 17, 17, 16, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 215 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 184) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CC(N)=O)c1ccccc1) `ZINC001721278869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721278869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721278869 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CC(N)=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 21, 21, 21, 44, 50, 50, 18, 24, 24, 18, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 44, 44, 50, 50, 24, 24, 18, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 243 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721278869 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721278869 Building ZINC001721287578 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721287578 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/185 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cn(C)nn2)C1) `ZINC001721287578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721287578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721287578 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 26, 26, 45, 45, 45, 45, 45, 15, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 45, 45, 45, 45, 15, 15] 50 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/186 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cn(C)nn2)C1) `ZINC001721287578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721287578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721287578 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 26, 26, 47, 47, 47, 47, 47, 15, 9, 9, 9, 9, 9, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 47, 47, 47, 47, 15, 15] 50 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721287578 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 Building ZINC001721287578 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721287578 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 185) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cn(C)nn2)C1) `ZINC001721287578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721287578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721287578 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 26, 26, 45, 45, 45, 45, 45, 15, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 45, 45, 45, 45, 15, 15] 50 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 186) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cn(C)nn2)C1) `ZINC001721287578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721287578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721287578 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 26, 26, 47, 47, 47, 47, 47, 15, 9, 9, 9, 9, 9, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 47, 47, 47, 47, 15, 15] 50 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721287578 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287578 Building ZINC001721287580 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721287580 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/187 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cn(C)nn2)C1) `ZINC001721287580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721287580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721287580 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 29, 29, 48, 48, 48, 48, 48, 13, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 48, 48, 48, 48, 13, 13] 50 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 142 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/188 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cn(C)nn2)C1) `ZINC001721287580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721287580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721287580 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 30, 30, 45, 45, 45, 45, 45, 11, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 45, 45, 45, 45, 11, 11] 50 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721287580 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 Building ZINC001721287580 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721287580 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 187) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cn(C)nn2)C1) `ZINC001721287580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721287580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721287580 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 29, 29, 48, 48, 48, 48, 48, 13, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 48, 48, 48, 48, 13, 13] 50 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 142 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 188) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cn(C)nn2)C1) `ZINC001721287580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721287580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721287580 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 30, 30, 45, 45, 45, 45, 45, 11, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 45, 45, 45, 45, 11, 11] 50 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721287580 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721287580 Building ZINC001721288720 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721288720 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/189 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ncn(C)n1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721288720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721288720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721288720 none CCCN(C(=O)c1ncn(C)n1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 4, 11, 23, 23, 47, 47, 47, 47, 47, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 47, 47, 47, 47, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/190 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ncn(C)n1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721288720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721288720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721288720 none CCCN(C(=O)c1ncn(C)n1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 12, 3, 12, 26, 26, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 15, 15, 15, 48, 48, 48, 48, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721288720 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 Building ZINC001721288720 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721288720 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 189) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ncn(C)n1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721288720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721288720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721288720 none CCCN(C(=O)c1ncn(C)n1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 4, 11, 23, 23, 47, 47, 47, 47, 47, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 47, 47, 47, 47, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 190) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ncn(C)n1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721288720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721288720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721288720 none CCCN(C(=O)c1ncn(C)n1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 12, 3, 12, 26, 26, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 15, 15, 15, 48, 48, 48, 48, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721288720 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288720 Building ZINC001721288721 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721288721 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/191 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ncn(C)n1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721288721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721288721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721288721 none CCCN(C(=O)c1ncn(C)n1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 12, 3, 12, 26, 26, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 15, 15, 15, 48, 48, 48, 48, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/192 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ncn(C)n1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721288721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721288721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721288721 none CCCN(C(=O)c1ncn(C)n1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 12, 4, 12, 25, 25, 46, 46, 46, 46, 46, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 15, 15, 15, 46, 46, 46, 46, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721288721 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 Building ZINC001721288721 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721288721 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 191) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ncn(C)n1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721288721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721288721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721288721 none CCCN(C(=O)c1ncn(C)n1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 12, 3, 12, 26, 26, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 15, 15, 15, 48, 48, 48, 48, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 192) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ncn(C)n1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721288721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721288721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721288721 none CCCN(C(=O)c1ncn(C)n1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 12, 4, 12, 25, 25, 46, 46, 46, 46, 46, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 15, 15, 15, 46, 46, 46, 46, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721288721 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721288721 Building ZINC001721294484 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721294484 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/193 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721294484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721294484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721294484 none CSCC(=O)N1CCN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 35, 29, 35, 29, 29, 29, 11, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 41, 41, 29, 29, 29, 29, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/194 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721294484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721294484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721294484 none CSCC(=O)N1CCN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 34, 29, 34, 29, 29, 29, 12, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 41, 41, 29, 29, 29, 29, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 144 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721294484 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 Building ZINC001721294484 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721294484 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 193) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721294484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721294484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721294484 none CSCC(=O)N1CCN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 35, 29, 35, 29, 29, 29, 11, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 41, 41, 29, 29, 29, 29, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 194) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721294484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721294484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721294484 none CSCC(=O)N1CCN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 34, 29, 34, 29, 29, 29, 12, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 41, 41, 29, 29, 29, 29, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 144 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721294484 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721294484 Building ZINC001721298311 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721298311 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/195 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N(C)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721298311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721298311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721298311 none CNC(=O)CC(=O)N(C)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 23, 19, 23, 11, 19, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 49, 49, 19, 19, 19, 11, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/196 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N(C)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721298311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721298311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721298311 none CNC(=O)CC(=O)N(C)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 23, 17, 23, 11, 17, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 47, 47, 17, 17, 17, 11, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721298311 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 Building ZINC001721298311 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721298311 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 195) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N(C)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721298311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721298311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721298311 none CNC(=O)CC(=O)N(C)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 23, 19, 23, 11, 19, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 49, 49, 19, 19, 19, 11, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 196) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N(C)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721298311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721298311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721298311 none CNC(=O)CC(=O)N(C)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 23, 17, 23, 11, 17, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 47, 47, 17, 17, 17, 11, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721298311 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298311 Building ZINC001721298312 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721298312 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/197 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N(C)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721298312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721298312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721298312 none CNC(=O)CC(=O)N(C)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 22, 16, 22, 10, 16, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 49, 49, 16, 16, 16, 10, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/198 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N(C)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721298312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721298312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721298312 none CNC(=O)CC(=O)N(C)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 21, 19, 21, 11, 19, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 49, 49, 19, 19, 19, 11, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721298312 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 Building ZINC001721298312 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721298312 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 197) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CC(=O)N(C)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721298312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721298312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721298312 none CNC(=O)CC(=O)N(C)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 22, 16, 22, 10, 16, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 49, 49, 16, 16, 16, 10, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 198) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CC(=O)N(C)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721298312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721298312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721298312 none CNC(=O)CC(=O)N(C)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 21, 19, 21, 11, 19, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 49, 49, 19, 19, 19, 11, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721298312 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721298312 Building ZINC001721299553 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721299553 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/199 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721299553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721299553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721299553 none CN(C[C@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/200 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721299553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721299553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721299553 none CN(C[C@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 15, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721299553 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 Building ZINC001721299553 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721299553 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 199) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721299553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721299553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721299553 none CN(C[C@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 200) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721299553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721299553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721299553 none CN(C[C@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 15, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721299553 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299553 Building ZINC001721299554 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721299554 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/201 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721299554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721299554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721299554 none CN(C[C@@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 15, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/202 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721299554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721299554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721299554 none CN(C[C@@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721299554 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 Building ZINC001721299554 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721299554 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 201) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721299554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721299554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721299554 none CN(C[C@@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 15, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 202) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721299554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721299554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721299554 none CN(C[C@@H]1CCN(C(=O)c2cc[n+]([O-])cc2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721299554 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721299554 Building ZINC001721301665 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721301665 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/203 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721301665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721301665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301665 none CN(C[C@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 12, 16, 16, 16, 16, 16, 26, 38, 50, 50, 50, 50, 50, 50, 16, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/204 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721301665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721301665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301665 none CN(C[C@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 11, 20, 20, 20, 20, 20, 24, 36, 50, 50, 50, 50, 50, 50, 20, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721301665 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 Building ZINC001721301665 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721301665 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 203) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721301665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721301665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301665 none CN(C[C@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 12, 16, 16, 16, 16, 16, 26, 38, 50, 50, 50, 50, 50, 50, 16, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 204) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721301665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721301665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301665 none CN(C[C@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 11, 20, 20, 20, 20, 20, 24, 36, 50, 50, 50, 50, 50, 50, 20, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721301665 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301665 Building ZINC001721301666 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721301666 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/205 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721301666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721301666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301666 none CN(C[C@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 10, 19, 19, 19, 19, 19, 28, 38, 50, 50, 50, 50, 50, 50, 19, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/206 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721301666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721301666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301666 none CN(C[C@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 11, 18, 18, 18, 18, 18, 25, 36, 50, 50, 50, 50, 50, 50, 18, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721301666 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 Building ZINC001721301666 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721301666 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 205) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721301666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721301666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301666 none CN(C[C@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 10, 19, 19, 19, 19, 19, 28, 38, 50, 50, 50, 50, 50, 50, 19, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 206) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721301666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721301666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301666 none CN(C[C@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 11, 18, 18, 18, 18, 18, 25, 36, 50, 50, 50, 50, 50, 50, 18, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721301666 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301666 Building ZINC001721301667 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721301667 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/207 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721301667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721301667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301667 none CN(C[C@@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 20, 20, 20, 20, 20, 26, 36, 50, 50, 50, 50, 50, 50, 20, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/208 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721301667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721301667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301667 none CN(C[C@@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 12, 21, 21, 21, 21, 21, 30, 40, 50, 50, 50, 50, 50, 50, 21, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721301667 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 Building ZINC001721301667 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721301667 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 207) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721301667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721301667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301667 none CN(C[C@@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 20, 20, 20, 20, 20, 26, 36, 50, 50, 50, 50, 50, 50, 20, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 208) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721301667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721301667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301667 none CN(C[C@@H]1CCN(C(=O)[C@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 12, 21, 21, 21, 21, 21, 30, 40, 50, 50, 50, 50, 50, 50, 21, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721301667 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301667 Building ZINC001721301668 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721301668 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/209 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721301668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721301668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301668 none CN(C[C@@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 9, 18, 18, 18, 18, 18, 23, 35, 50, 50, 50, 50, 50, 50, 18, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/210 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721301668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721301668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301668 none CN(C[C@@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 9, 16, 16, 16, 16, 16, 26, 38, 50, 50, 50, 50, 50, 50, 16, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721301668 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 Building ZINC001721301668 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721301668 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 209) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721301668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721301668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301668 none CN(C[C@@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 9, 18, 18, 18, 18, 18, 23, 35, 50, 50, 50, 50, 50, 50, 18, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 210) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721301668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721301668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721301668 none CN(C[C@@H]1CCN(C(=O)[C@@H]2COCCO2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 9, 16, 16, 16, 16, 16, 26, 38, 50, 50, 50, 50, 50, 50, 16, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721301668 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721301668 Building ZINC001721308094 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721308094 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/211 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721308094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721308094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721308094 none CN(C[C@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 14, 21, 21, 21, 21, 21, 31, 31, 50, 50, 50, 50, 50, 50, 21, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 21, 21, 21, 21, 50, 100, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 235 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/212 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721308094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721308094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721308094 none CN(C[C@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 13, 20, 20, 20, 20, 20, 29, 29, 50, 50, 50, 50, 50, 50, 20, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 20, 20, 20, 20, 50, 100, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721308094 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 Building ZINC001721308094 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721308094 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 211) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721308094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721308094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721308094 none CN(C[C@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 14, 21, 21, 21, 21, 21, 31, 31, 50, 50, 50, 50, 50, 50, 21, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 21, 21, 21, 21, 50, 100, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 235 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 212) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721308094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721308094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721308094 none CN(C[C@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 13, 20, 20, 20, 20, 20, 29, 29, 50, 50, 50, 50, 50, 50, 20, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 20, 20, 20, 20, 50, 100, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721308094 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308094 Building ZINC001721308095 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721308095 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/213 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721308095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721308095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721308095 none CN(C[C@@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 13, 21, 21, 21, 21, 21, 29, 29, 50, 50, 50, 50, 50, 50, 21, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 21, 21, 21, 21, 50, 100, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/214 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721308095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721308095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721308095 none CN(C[C@@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 14, 23, 23, 23, 23, 23, 33, 33, 50, 50, 50, 50, 50, 50, 23, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 23, 23, 23, 23, 50, 100, 50, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 241 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721308095 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 Building ZINC001721308095 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721308095 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 213) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721308095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721308095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721308095 none CN(C[C@@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 13, 21, 21, 21, 21, 21, 29, 29, 50, 50, 50, 50, 50, 50, 21, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 21, 21, 21, 21, 50, 100, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 214) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721308095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721308095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721308095 none CN(C[C@@H]1CCN(C(=O)c2cnnc(O)c2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 12, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 3, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 14, 23, 23, 23, 23, 23, 33, 33, 50, 50, 50, 50, 50, 50, 23, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 23, 23, 23, 23, 50, 100, 50, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 241 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721308095 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721308095 Building ZINC001721309058 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721309058 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/215 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721309058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721309058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721309058 none CN(C[C@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 15, 27, 27, 27, 27, 27, 44, 44, 50, 50, 50, 50, 50, 27, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 27, 27, 27, 27, 50, 50, 50, 50, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/216 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721309058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721309058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721309058 none CN(C[C@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 26, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 26, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 26, 26, 26, 26, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721309058 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 Building ZINC001721309058 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721309058 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 215) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721309058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721309058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721309058 none CN(C[C@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 15, 27, 27, 27, 27, 27, 44, 44, 50, 50, 50, 50, 50, 27, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 27, 27, 27, 27, 50, 50, 50, 50, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 216) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721309058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721309058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721309058 none CN(C[C@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 26, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 26, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 26, 26, 26, 26, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721309058 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309058 Building ZINC001721309059 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721309059 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/217 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721309059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721309059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721309059 none CN(C[C@@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 26, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 26, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 26, 26, 26, 26, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/218 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721309059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721309059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721309059 none CN(C[C@@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 15, 28, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 28, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721309059 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 Building ZINC001721309059 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721309059 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 217) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721309059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721309059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721309059 none CN(C[C@@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 26, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 26, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 26, 26, 26, 26, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 218) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721309059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721309059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721309059 none CN(C[C@@H]1CCN(C(=O)c2cnn(C)n2)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 15, 28, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 28, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721309059 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721309059 Building ZINC001721311214 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721311214 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/219 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721311214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721311214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311214 none CN(C[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 26, 26, 26, 26, 26, 34, 37, 50, 50, 50, 50, 50, 50, 26, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 26, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/220 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721311214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721311214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311214 none CN(C[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 24, 24, 24, 24, 24, 36, 39, 50, 50, 50, 50, 50, 50, 24, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 165 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721311214 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 Building ZINC001721311214 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721311214 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 219) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721311214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721311214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311214 none CN(C[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 26, 26, 26, 26, 26, 34, 37, 50, 50, 50, 50, 50, 50, 26, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 26, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 220) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721311214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721311214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311214 none CN(C[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 24, 24, 24, 24, 24, 36, 39, 50, 50, 50, 50, 50, 50, 24, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 165 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721311214 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311214 Building ZINC001721311215 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721311215 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/221 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721311215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721311215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311215 none CN(C[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 24, 24, 24, 24, 24, 36, 42, 50, 50, 50, 50, 50, 50, 24, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/222 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721311215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721311215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311215 none CN(C[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 26, 26, 26, 26, 26, 34, 39, 50, 50, 50, 50, 50, 50, 26, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 26, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721311215 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 Building ZINC001721311215 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721311215 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 221) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721311215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721311215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311215 none CN(C[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 24, 24, 24, 24, 24, 36, 42, 50, 50, 50, 50, 50, 50, 24, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 222) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721311215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721311215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311215 none CN(C[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 26, 26, 26, 26, 26, 34, 39, 50, 50, 50, 50, 50, 50, 26, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 26, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721311215 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311215 Building ZINC001721311216 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721311216 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/223 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721311216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721311216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311216 none CN(C[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 23, 23, 23, 23, 23, 33, 37, 50, 50, 50, 50, 50, 50, 23, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 23, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/224 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721311216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721311216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311216 none CN(C[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 22, 22, 22, 22, 22, 35, 36, 50, 50, 50, 50, 50, 50, 22, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721311216 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 Building ZINC001721311216 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721311216 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 223) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721311216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721311216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311216 none CN(C[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 23, 23, 23, 23, 23, 33, 37, 50, 50, 50, 50, 50, 50, 23, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 23, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 224) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721311216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721311216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311216 none CN(C[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 22, 22, 22, 22, 22, 35, 36, 50, 50, 50, 50, 50, 50, 22, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721311216 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311216 Building ZINC001721311217 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721311217 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/225 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721311217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721311217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311217 none CN(C[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 22, 22, 22, 22, 22, 35, 36, 50, 50, 50, 50, 50, 50, 22, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/226 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721311217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721311217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311217 none CN(C[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 22, 22, 22, 22, 22, 34, 39, 50, 50, 50, 50, 50, 50, 22, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721311217 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 Building ZINC001721311217 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721311217 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 225) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721311217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721311217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311217 none CN(C[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 13, 22, 22, 22, 22, 22, 35, 36, 50, 50, 50, 50, 50, 50, 22, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 226) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721311217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721311217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721311217 none CN(C[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 14, 22, 22, 22, 22, 22, 34, 39, 50, 50, 50, 50, 50, 50, 22, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721311217 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721311217 Building ZINC001721320566 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721320566 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/227 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCn2cccn2)C1) `ZINC001721320566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721320566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721320566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 13, 13, 13, 35, 43, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 35, 35, 43, 43, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/228 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCn2cccn2)C1) `ZINC001721320566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721320566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721320566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 26, 37, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 26, 26, 37, 37, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721320566 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 Building ZINC001721320566 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721320566 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 227) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCn2cccn2)C1) `ZINC001721320566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721320566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721320566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 13, 13, 13, 35, 43, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 35, 35, 43, 43, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 228) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCn2cccn2)C1) `ZINC001721320566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721320566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721320566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 26, 37, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 26, 26, 37, 37, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721320566 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320566 Building ZINC001721320632 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721320632 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/229 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCS(C)(=O)=O)C1) `ZINC001721320632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721320632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721320632 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 15, 15, 15, 35, 35, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 15, 35, 35, 35, 35, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/230 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCS(C)(=O)=O)C1) `ZINC001721320632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721320632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721320632 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 7, 7, 7, 7, 7, 7, 15, 15, 15, 35, 36, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 15, 35, 35, 36, 36, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721320632 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 Building ZINC001721320632 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721320632 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 229) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCS(C)(=O)=O)C1) `ZINC001721320632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721320632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721320632 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 15, 15, 15, 35, 35, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 15, 35, 35, 35, 35, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 230) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCS(C)(=O)=O)C1) `ZINC001721320632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721320632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721320632 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 7, 7, 7, 7, 7, 7, 15, 15, 15, 35, 36, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 15, 35, 35, 36, 36, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721320632 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320632 Building ZINC001721320656 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721320656 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/231 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721320656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721320656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721320656 none CCNC(=O)CC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 30, 33, 9, 9, 9, 4, 4, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 33, 30, 30, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/232 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721320656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721320656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721320656 none CCNC(=O)CC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 26, 35, 9, 9, 9, 4, 4, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 35, 26, 26, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721320656 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 Building ZINC001721320656 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721320656 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 231) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721320656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721320656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721320656 none CCNC(=O)CC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 30, 33, 9, 9, 9, 4, 4, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 33, 30, 30, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 232) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721320656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721320656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721320656 none CCNC(=O)CC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 26, 35, 9, 9, 9, 4, 4, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 35, 26, 26, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721320656 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320656 Building ZINC001721320699 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721320699 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/233 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721320699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721320699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721320699 none COCCOCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 31, 17, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 46, 46, 17, 17, 6, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/234 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721320699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721320699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721320699 none COCCOCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 31, 13, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 44, 44, 13, 13, 4, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721320699 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 Building ZINC001721320699 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721320699 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 233) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721320699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721320699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721320699 none COCCOCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 31, 17, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 46, 46, 17, 17, 6, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 234) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721320699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721320699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721320699 none COCCOCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 31, 13, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 44, 44, 13, 13, 4, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721320699 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721320699 Building ZINC001721321971 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721321971 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/235 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)[C@H]2CCCC(=O)N2)C1) `ZINC001721321971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721321971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721321971 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 21, 21, 21, 21, 21, 21, 32, 39, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/236 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)[C@H]2CCCC(=O)N2)C1) `ZINC001721321971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721321971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721321971 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 20, 20, 20, 20, 20, 33, 43, 50, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721321971 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 Building ZINC001721321971 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721321971 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 235) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)[C@H]2CCCC(=O)N2)C1) `ZINC001721321971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721321971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721321971 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 21, 21, 21, 21, 21, 21, 32, 39, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 236) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)[C@H]2CCCC(=O)N2)C1) `ZINC001721321971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721321971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721321971 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 20, 20, 20, 20, 20, 33, 43, 50, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721321971 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721321971 Building ZINC001721322590 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721322590 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/237 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001721322590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721322590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721322590 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 22, 22, 22, 22, 22, 22, 36, 36, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/238 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001721322590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721322590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721322590 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 25, 25, 25, 25, 25, 25, 38, 38, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721322590 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 Building ZINC001721322590 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721322590 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 237) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001721322590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721322590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721322590 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 22, 22, 22, 22, 22, 22, 36, 36, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 238) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001721322590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721322590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721322590 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 25, 25, 25, 25, 25, 25, 38, 38, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721322590 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721322590 Building ZINC001721323571 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721323571 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/239 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001721323571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721323571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721323571 none CCn1cc(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 24, 12, 24, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 38, 38, 50, 50, 50, 50, 50, 38, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/240 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001721323571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721323571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721323571 none CCn1cc(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 25, 14, 25, 14, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 37, 37, 50, 50, 50, 50, 50, 37, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721323571 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 Building ZINC001721323571 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721323571 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 239) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001721323571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721323571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721323571 none CCn1cc(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 24, 12, 24, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 38, 38, 50, 50, 50, 50, 50, 38, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 240) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001721323571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721323571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721323571 none CCn1cc(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 25, 14, 25, 14, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 37, 37, 50, 50, 50, 50, 50, 37, 14, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721323571 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323571 Building ZINC001721323664 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721323664 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/241 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncc(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001721323664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721323664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721323664 none COc1ncc(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 41, 50, 50, 39, 21, 39, 21, 21, 21, 21, 6, 21, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/242 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncc(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001721323664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721323664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721323664 none COc1ncc(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 43, 50, 50, 42, 21, 42, 21, 21, 21, 21, 6, 21, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721323664 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 Building ZINC001721323664 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721323664 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 241) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncc(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001721323664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721323664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721323664 none COc1ncc(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 41, 50, 50, 39, 21, 39, 21, 21, 21, 21, 6, 21, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 242) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncc(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001721323664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721323664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721323664 none COc1ncc(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 43, 50, 50, 42, 21, 42, 21, 21, 21, 21, 6, 21, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721323664 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721323664 Building ZINC001721334167 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334167 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/243 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccn3c2)C1) `ZINC001721334167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334167 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/244 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccn3c2)C1) `ZINC001721334167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334167 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334167 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 Building ZINC001721334167 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334167 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 243) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccn3c2)C1) `ZINC001721334167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334167 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 244) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccn3c2)C1) `ZINC001721334167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334167 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334167 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334167 Building ZINC001721334180 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334180 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/245 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccnc3c2)C1) `ZINC001721334180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334180 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/246 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccnc3c2)C1) `ZINC001721334180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334180 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 17, 17, 17, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334180 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 Building ZINC001721334180 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334180 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 245) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccnc3c2)C1) `ZINC001721334180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334180 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 246) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccnc3c2)C1) `ZINC001721334180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334180 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3nccnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 17, 17, 17, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334180 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334180 Building ZINC001721334205 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334205 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/247 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc2cncc(C(=O)N3CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)c21) `ZINC001721334205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334205 none Cn1cnc2cncc(C(=O)N3CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 34, 21, 34, 21, 21, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/248 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc2cncc(C(=O)N3CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)c21) `ZINC001721334205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334205 none Cn1cnc2cncc(C(=O)N3CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 32, 21, 32, 21, 21, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334205 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 Building ZINC001721334205 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334205 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 247) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc2cncc(C(=O)N3CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)c21) `ZINC001721334205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334205 none Cn1cnc2cncc(C(=O)N3CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 34, 21, 34, 21, 21, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 248) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc2cncc(C(=O)N3CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)c21) `ZINC001721334205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334205 none Cn1cnc2cncc(C(=O)N3CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 32, 21, 32, 21, 21, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334205 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334205 Building ZINC001721334210 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334210 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/249 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(CC(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001721334210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721334210 none CCc1cc(CC(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 21, 5, 4, 5, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 29, 29, 29, 50, 50, 50, 50, 50, 29, 21, 21, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 29, 29, 29] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/250 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(CC(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001721334210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721334210 none CCc1cc(CC(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 19, 4, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 28, 50, 50, 50, 50, 50, 28, 19, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 28, 28, 28] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 43, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334210 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 Building ZINC001721334210 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334210 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 249) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(CC(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001721334210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721334210 none CCc1cc(CC(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 21, 5, 4, 5, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 29, 29, 29, 50, 50, 50, 50, 50, 29, 21, 21, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 29, 29, 29] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 250) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(CC(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001721334210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721334210 none CCc1cc(CC(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 19, 4, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 28, 50, 50, 50, 50, 50, 28, 19, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 28, 28, 28] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 43, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334210 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334210 Building ZINC001721334227 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334227 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/251 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc2ncc(C(=O)N3CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)cc12) `ZINC001721334227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334227 none Cc1[nH]nc2ncc(C(=O)N3CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 17, 26, 17, 17, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/252 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc2ncc(C(=O)N3CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)cc12) `ZINC001721334227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334227 none Cc1[nH]nc2ncc(C(=O)N3CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 19, 31, 19, 19, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334227 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 Building ZINC001721334227 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334227 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 251) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc2ncc(C(=O)N3CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)cc12) `ZINC001721334227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334227 none Cc1[nH]nc2ncc(C(=O)N3CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 17, 26, 17, 17, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 252) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc2ncc(C(=O)N3CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)cc12) `ZINC001721334227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334227 none Cc1[nH]nc2ncc(C(=O)N3CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 19, 31, 19, 19, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334227 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334227 Building ZINC001721334245 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334245 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/253 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)CCc2nc(C3CC3)no2)C1) `ZINC001721334245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721334245 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)CCc2nc(C3CC3)no2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 13, 15, 38, 38, 38, 50, 50, 38, 38, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 15, 15, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/254 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)CCc2nc(C3CC3)no2)C1) `ZINC001721334245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721334245 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)CCc2nc(C3CC3)no2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 7, 7, 16, 19, 39, 39, 39, 50, 50, 39, 39, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 16, 16, 19, 19, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334245 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 Building ZINC001721334245 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334245 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 253) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)CCc2nc(C3CC3)no2)C1) `ZINC001721334245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721334245 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)CCc2nc(C3CC3)no2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 13, 15, 38, 38, 38, 50, 50, 38, 38, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 15, 15, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 254) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)CCc2nc(C3CC3)no2)C1) `ZINC001721334245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721334245 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)CCc2nc(C3CC3)no2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 7, 7, 16, 19, 39, 39, 39, 50, 50, 39, 39, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 16, 16, 19, 19, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334245 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334245 Building ZINC001721334270 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334270 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/255 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@H](C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1) `ZINC001721334270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334270 none CN(C)[C@H](C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 28, 15, 26, 8, 15, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 26, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/256 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@H](C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1) `ZINC001721334270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334270 none CN(C)[C@H](C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 30, 17, 28, 7, 17, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 28, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334270 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 Building ZINC001721334270 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334270 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 255) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@H](C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1) `ZINC001721334270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334270 none CN(C)[C@H](C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 28, 15, 26, 8, 15, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 26, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 256) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@H](C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1) `ZINC001721334270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334270 none CN(C)[C@H](C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 30, 17, 28, 7, 17, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 28, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334270 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334270 Building ZINC001721334271 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334271 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/257 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H](C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1) `ZINC001721334271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334271 none CN(C)[C@@H](C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 32, 19, 29, 8, 19, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 29, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/258 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H](C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1) `ZINC001721334271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334271 none CN(C)[C@@H](C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 27, 16, 25, 8, 16, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 25, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334271 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 Building ZINC001721334271 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334271 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 257) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H](C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1) `ZINC001721334271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334271 none CN(C)[C@@H](C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 32, 19, 29, 8, 19, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 29, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 258) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H](C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1) `ZINC001721334271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334271 none CN(C)[C@@H](C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 27, 16, 25, 8, 16, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 25, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334271 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334271 Building ZINC001721334297 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334297 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/259 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(C(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1) `ZINC001721334297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334297 none Cc1cc(C)c(C(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 17, 34, 17, 17, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 100] 100 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/260 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(C(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1) `ZINC001721334297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334297 none Cc1cc(C)c(C(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 35, 22, 35, 22, 22, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 100] 100 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334297 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 Building ZINC001721334297 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334297 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 259) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(C(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1) `ZINC001721334297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334297 none Cc1cc(C)c(C(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 17, 34, 17, 17, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 100] 100 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 260) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(C(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1) `ZINC001721334297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334297 none Cc1cc(C)c(C(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 35, 22, 35, 22, 22, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 100] 100 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334297 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334297 Building ZINC001721334307 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334307 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/261 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)C2(CF)CCOCC2)C1) `ZINC001721334307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334307 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)C2(CF)CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 26, 37, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/262 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)C2(CF)CCOCC2)C1) `ZINC001721334307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334307 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)C2(CF)CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 25, 38, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334307 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 Building ZINC001721334307 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334307 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 261) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)C2(CF)CCOCC2)C1) `ZINC001721334307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334307 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)C2(CF)CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 26, 37, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 262) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)C2(CF)CCOCC2)C1) `ZINC001721334307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334307 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)C2(CF)CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 25, 38, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334307 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334307 Building ZINC001721334313 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334313 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/263 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCCC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721334313 none CC(C)(C)C(=O)NCCC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 23, 6, 4, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 23, 23, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 45, 50, 49, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/264 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCCC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721334313 none CC(C)(C)C(=O)NCCC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 25, 7, 5, 7, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 25, 25, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334313 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 Building ZINC001721334313 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334313 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 263) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCCC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721334313 none CC(C)(C)C(=O)NCCC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 23, 6, 4, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 23, 23, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 45, 50, 49, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 264) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCCC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721334313 none CC(C)(C)C(=O)NCCC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 25, 7, 5, 7, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 25, 25, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334313 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334313 Building ZINC001721334332 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334332 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/265 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334332 none CC[C@@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 22, 43, 10, 22, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 139 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/266 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334332 none CC[C@@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 21, 43, 10, 21, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 141 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334332 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 Building ZINC001721334332 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334332 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 265) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334332 none CC[C@@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 22, 43, 10, 22, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 139 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 266) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334332 none CC[C@@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 21, 43, 10, 21, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 141 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334332 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334332 Building ZINC001721334333 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334333 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/267 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334333 none CC[C@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 25, 44, 10, 25, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/268 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334333 none CC[C@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 20, 43, 10, 20, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 144 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334333 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 Building ZINC001721334333 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334333 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 267) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334333 none CC[C@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 25, 44, 10, 25, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 268) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721334333 none CC[C@H]1CCCN1C(=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 20, 43, 10, 20, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 144 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334333 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334333 Building ZINC001721334335 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334335 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/269 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCn3cncc3C2)C1) `ZINC001721334335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334335 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCn3cncc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 20, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/270 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCn3cncc3C2)C1) `ZINC001721334335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334335 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCn3cncc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 21, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334335 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 Building ZINC001721334335 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334335 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 269) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCn3cncc3C2)C1) `ZINC001721334335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334335 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCn3cncc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 20, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 270) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCn3cncc3C2)C1) `ZINC001721334335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334335 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCn3cncc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 21, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334335 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334335 Building ZINC001721334336 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334336 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/271 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCn3cncc3C2)C1) `ZINC001721334336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334336 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCn3cncc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 21, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/272 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCn3cncc3C2)C1) `ZINC001721334336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334336 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCn3cncc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 21, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334336 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 Building ZINC001721334336 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334336 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 271) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCn3cncc3C2)C1) `ZINC001721334336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334336 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCn3cncc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 21, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 272) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCn3cncc3C2)C1) `ZINC001721334336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334336 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCn3cncc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 21, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334336 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334336 Building ZINC001721334367 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334367 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/273 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ncc(F)cc2F)C1) `ZINC001721334367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001721334367 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ncc(F)cc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 26, 26, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/274 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ncc(F)cc2F)C1) `ZINC001721334367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001721334367 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ncc(F)cc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 26, 26, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334367 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 Building ZINC001721334367 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334367 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 273) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ncc(F)cc2F)C1) `ZINC001721334367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001721334367 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ncc(F)cc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 26, 26, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 274) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ncc(F)cc2F)C1) `ZINC001721334367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001721334367 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ncc(F)cc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 1, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 26, 26, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334367 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334367 Building ZINC001721334387 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334387 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/275 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc(C3CC3)nc2)C1) `ZINC001721334387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334387 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc(C3CC3)nc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 18, 18, 18, 24, 24, 38, 38, 24, 24, 50, 50, 38, 38, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 38, 50, 50, 50, 50, 50, 38, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/276 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/276' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc(C3CC3)nc2)C1) `ZINC001721334387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334387 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc(C3CC3)nc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 23, 23, 38, 38, 38, 38, 50, 50, 38, 38, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 38, 50, 50, 50, 50, 50, 38, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334387 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 Building ZINC001721334387 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334387 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 275) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc(C3CC3)nc2)C1) `ZINC001721334387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334387 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc(C3CC3)nc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 18, 18, 18, 24, 24, 38, 38, 24, 24, 50, 50, 38, 38, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 38, 50, 50, 50, 50, 50, 38, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 276) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc(C3CC3)nc2)C1) `ZINC001721334387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721334387 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc(C3CC3)nc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 23, 23, 38, 38, 38, 38, 50, 50, 38, 38, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 38, 50, 50, 50, 50, 50, 38, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334387 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334387 Building ZINC001721334389 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334389 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/277 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C(F)F)cc1C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334389 none Cn1nc(C(F)F)cc1C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 50, 50, 43, 26, 17, 26, 17, 17, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 43, 43, 43, 50, 43, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/278 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C(F)F)cc1C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334389 none Cn1nc(C(F)F)cc1C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 50, 50, 42, 26, 15, 26, 15, 15, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 42, 42, 42, 50, 42, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334389 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 Building ZINC001721334389 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334389 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 277) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C(F)F)cc1C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334389 none Cn1nc(C(F)F)cc1C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 50, 50, 43, 26, 17, 26, 17, 17, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 43, 43, 43, 50, 43, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 278) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C(F)F)cc1C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334389 none Cn1nc(C(F)F)cc1C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 50, 50, 42, 26, 15, 26, 15, 15, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 42, 42, 42, 50, 42, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334389 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334389 Building ZINC001721334402 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334402 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/279 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cn3ccccc3n2)C1) `ZINC001721334402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334402 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cn3ccccc3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 19, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 50, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/280 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cn3ccccc3n2)C1) `ZINC001721334402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334402 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cn3ccccc3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 23, 23, 23, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334402 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 Building ZINC001721334402 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334402 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 279) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cn3ccccc3n2)C1) `ZINC001721334402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334402 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cn3ccccc3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 19, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 50, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 280) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cn3ccccc3n2)C1) `ZINC001721334402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334402 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cn3ccccc3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 23, 23, 23, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334402 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334402 Building ZINC001721334405 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334405 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/281 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3[nH]c(O)nc3c2)C1) `ZINC001721334405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334405 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3[nH]c(O)nc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 18, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 50, 150, 50, 18, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/282 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3[nH]c(O)nc3c2)C1) `ZINC001721334405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334405 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3[nH]c(O)nc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 19, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 50, 150, 50, 19, 19] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334405 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 Building ZINC001721334405 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334405 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 281) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3[nH]c(O)nc3c2)C1) `ZINC001721334405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334405 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3[nH]c(O)nc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 18, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 50, 150, 50, 18, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 282) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3[nH]c(O)nc3c2)C1) `ZINC001721334405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334405 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cnc3[nH]c(O)nc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 19, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 50, 150, 50, 19, 19] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334405 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334405 Building ZINC001721334422 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334422 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/283 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c2C(F)(F)F)C1) `ZINC001721334422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001721334422 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 17, 17, 17, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/284 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c2C(F)(F)F)C1) `ZINC001721334422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001721334422 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 17, 17, 17, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334422 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 Building ZINC001721334422 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334422 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 283) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c2C(F)(F)F)C1) `ZINC001721334422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001721334422 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 17, 17, 17, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 284) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c2C(F)(F)F)C1) `ZINC001721334422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001721334422 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 17, 17, 17, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334422 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334422 Building ZINC001721334438 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334438 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/285 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721334438 none CC(C)(C)[C@@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 50, 31, 47, 47, 50, 50, 50, 11, 31, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/286 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721334438 none CC(C)(C)[C@@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 49, 32, 46, 46, 50, 50, 50, 10, 32, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 49, 49, 49, 49, 49, 49, 49, 49, 49, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334438 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 Building ZINC001721334438 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334438 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 285) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721334438 none CC(C)(C)[C@@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 50, 31, 47, 47, 50, 50, 50, 11, 31, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 286) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721334438 none CC(C)(C)[C@@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 49, 32, 46, 46, 50, 50, 50, 10, 32, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 49, 49, 49, 49, 49, 49, 49, 49, 49, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334438 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334438 Building ZINC001721334439 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334439 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/287 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721334439 none CC(C)(C)[C@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 49, 33, 46, 46, 50, 50, 50, 9, 33, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/288 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721334439 none CC(C)(C)[C@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 50, 31, 49, 49, 50, 50, 50, 10, 31, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 189 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334439 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 Building ZINC001721334439 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334439 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 287) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721334439 none CC(C)(C)[C@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 49, 33, 46, 46, 50, 50, 50, 9, 33, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 288) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721334439 none CC(C)(C)[C@H](NC(N)=O)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 50, 31, 49, 49, 50, 50, 50, 10, 31, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 189 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334439 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334439 Building ZINC001721334456 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334456 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/289 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCCc3nn[nH]c32)C1) `ZINC001721334456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334456 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCCc3nn[nH]c32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 25, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/290 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCCc3nn[nH]c32)C1) `ZINC001721334456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334456 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCCc3nn[nH]c32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 27, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334456 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 Building ZINC001721334456 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334456 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 289) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCCc3nn[nH]c32)C1) `ZINC001721334456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334456 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCCc3nn[nH]c32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 25, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 290) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCCc3nn[nH]c32)C1) `ZINC001721334456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334456 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@H]2CCCc3nn[nH]c32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 27, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334456 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334456 Building ZINC001721334457 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334457 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/291 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCCc3nn[nH]c32)C1) `ZINC001721334457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334457 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCCc3nn[nH]c32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 27, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/292 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCCc3nn[nH]c32)C1) `ZINC001721334457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334457 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCCc3nn[nH]c32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 24, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334457 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 Building ZINC001721334457 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334457 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 291) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCCc3nn[nH]c32)C1) `ZINC001721334457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334457 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCCc3nn[nH]c32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 27, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 292) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCCc3nn[nH]c32)C1) `ZINC001721334457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334457 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)[C@@H]2CCCc3nn[nH]c32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 24, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334457 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334457 Building ZINC001721334463 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334463 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/293 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnn2CC(F)F)C1) `ZINC001721334463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334463 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnn2CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 15, 15, 15, 20, 20, 36, 36, 36, 36, 36, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 36, 36, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/294 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnn2CC(F)F)C1) `ZINC001721334463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334463 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnn2CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 17, 17, 31, 31, 31, 31, 31, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 31, 31, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334463 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 Building ZINC001721334463 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334463 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 293) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnn2CC(F)F)C1) `ZINC001721334463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334463 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnn2CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 15, 15, 15, 20, 20, 36, 36, 36, 36, 36, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 36, 36, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 294) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnn2CC(F)F)C1) `ZINC001721334463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334463 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnn2CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 17, 17, 31, 31, 31, 31, 31, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 31, 31, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334463 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334463 Building ZINC001721334471 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334471 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/295 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccc3nccn3c2)C1) `ZINC001721334471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334471 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/296 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccc3nccn3c2)C1) `ZINC001721334471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334471 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334471 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 Building ZINC001721334471 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334471 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 295) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccc3nccn3c2)C1) `ZINC001721334471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334471 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 296) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccc3nccn3c2)C1) `ZINC001721334471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334471 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334471 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334471 Building ZINC001721334481 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334481 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/297 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(=O)n1CC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334481 none Cc1csc(=O)n1CC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 10, 6, 10, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 34, 34, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/298 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(=O)n1CC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334481 none Cc1csc(=O)n1CC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 10, 6, 10, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 31, 31, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334481 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 Building ZINC001721334481 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334481 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 297) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(=O)n1CC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334481 none Cc1csc(=O)n1CC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 10, 6, 10, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 34, 34, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 298) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(=O)n1CC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334481 none Cc1csc(=O)n1CC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 10, 6, 10, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 31, 31, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334481 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334481 Building ZINC001721334508 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334508 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/299 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cccn3ccnc23)C1) `ZINC001721334508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334508 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cccn3ccnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/300 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cccn3ccnc23)C1) `ZINC001721334508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334508 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cccn3ccnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334508 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 Building ZINC001721334508 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334508 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 299) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cccn3ccnc23)C1) `ZINC001721334508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334508 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cccn3ccnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 300) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cccn3ccnc23)C1) `ZINC001721334508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721334508 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cccn3ccnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334508 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334508 Building ZINC001721334682 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334682 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/301 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)c1ccco1)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334682 none C[C@H](NC(=O)c1ccco1)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 12, 32, 32, 45, 45, 45, 50, 50, 50, 50, 7, 12, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 32, 32, 32, 45, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/302 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)c1ccco1)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334682 none C[C@H](NC(=O)c1ccco1)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 11, 33, 33, 46, 46, 46, 50, 50, 50, 50, 7, 11, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 33, 33, 33, 46, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334682 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 Building ZINC001721334682 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334682 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 301) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)c1ccco1)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334682 none C[C@H](NC(=O)c1ccco1)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 12, 32, 32, 45, 45, 45, 50, 50, 50, 50, 7, 12, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 32, 32, 32, 45, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 302) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)c1ccco1)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721334682 none C[C@H](NC(=O)c1ccco1)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 11, 33, 33, 46, 46, 46, 50, 50, 50, 50, 7, 11, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 33, 33, 33, 46, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334682 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334682 Building ZINC001721334706 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334706 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/303 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cc3ncccn3n2)C1) `ZINC001721334706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334706 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 19, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/304 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/304' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cc3ncccn3n2)C1) `ZINC001721334706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334706 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 21, 21, 21, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 21, 21, 21, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334706 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 Building ZINC001721334706 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334706 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 303) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cc3ncccn3n2)C1) `ZINC001721334706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334706 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 19, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 304) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cc3ncccn3n2)C1) `ZINC001721334706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334706 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 21, 21, 21, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 21, 21, 21, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334706 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334706 Building ZINC001721334715 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334715 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/305 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721334715 none CC(=O)NCC(C)(C)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 24, 13, 24, 24, 6, 13, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 44, 44, 24, 24, 24, 24, 24, 24, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 225 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/306 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721334715 none CC(=O)NCC(C)(C)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 24, 15, 24, 24, 7, 15, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 45, 45, 24, 24, 24, 24, 24, 24, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 221 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334715 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 Building ZINC001721334715 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334715 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 305) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721334715 none CC(=O)NCC(C)(C)C(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 24, 13, 24, 24, 6, 13, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 44, 44, 24, 24, 24, 24, 24, 24, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 225 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 306) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721334715 none CC(=O)NCC(C)(C)C(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 24, 15, 24, 24, 7, 15, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 45, 45, 24, 24, 24, 24, 24, 24, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 221 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334715 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334715 Building ZINC001721334848 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334848 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/307 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCCC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721334848 none CCCNC(=O)CCCC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 23, 27, 14, 14, 5, 3, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 27, 21, 22, 18, 18, 14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 45, 50, 49, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/308 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCCC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721334848 none CCCNC(=O)CCCC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 24, 27, 15, 15, 6, 4, 6, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 27, 22, 23, 19, 19, 15, 15, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334848 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 Building ZINC001721334848 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334848 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 307) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCCC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721334848 none CCCNC(=O)CCCC(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 23, 27, 14, 14, 5, 3, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 27, 21, 22, 18, 18, 14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 45, 50, 49, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 308) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCCC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721334848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721334848 none CCCNC(=O)CCCC(=O)N1CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 24, 27, 15, 15, 6, 4, 6, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 27, 22, 23, 19, 19, 15, 15, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334848 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334848 Building ZINC001721334852 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334852 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/309 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CCC(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)on1) `ZINC001721334852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334852 none COc1cc(CCC(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 25, 25, 12, 6, 12, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/310 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/310' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CCC(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)on1) `ZINC001721334852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334852 none COc1cc(CCC(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 24, 10, 6, 10, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334852 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 Building ZINC001721334852 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334852 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 309) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CCC(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)on1) `ZINC001721334852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334852 none COc1cc(CCC(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 25, 25, 12, 6, 12, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 310) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CCC(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)on1) `ZINC001721334852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721334852 none COc1cc(CCC(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 24, 10, 6, 10, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334852 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334852 Building ZINC001721334867 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334867 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/311 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnc3[nH]cnc32)C1) `ZINC001721334867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334867 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnc3[nH]cnc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 18, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/312 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnc3[nH]cnc32)C1) `ZINC001721334867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334867 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnc3[nH]cnc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 19, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334867 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 Building ZINC001721334867 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721334867 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 311) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnc3[nH]cnc32)C1) `ZINC001721334867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721334867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334867 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnc3[nH]cnc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 18, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 312) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnc3[nH]cnc32)C1) `ZINC001721334867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721334867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721334867 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2ccnc3[nH]cnc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 19, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721334867 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721334867 Building ZINC001721335056 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721335056 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/313 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c3nccc2-3)C1) `ZINC001721335056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721335056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721335056 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c3nccc2-3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/314 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c3nccc2-3)C1) `ZINC001721335056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721335056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721335056 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c3nccc2-3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721335056 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 Building ZINC001721335056 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721335056 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 313) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c3nccc2-3)C1) `ZINC001721335056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721335056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721335056 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c3nccc2-3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 314) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c3nccc2-3)C1) `ZINC001721335056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721335056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001721335056 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)c2nc[nH]c3nccc2-3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721335056 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335056 Building ZINC001721335106 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721335106 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/315 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)Cc2cnn3ccccc23)C1) `ZINC001721335106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721335106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721335106 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)Cc2cnn3ccccc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 24, 50, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 24, 24, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/316 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)Cc2cnn3ccccc23)C1) `ZINC001721335106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721335106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721335106 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)Cc2cnn3ccccc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 6, 6, 25, 50, 50, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 25, 25, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721335106 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 Building ZINC001721335106 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721335106 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 315) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)Cc2cnn3ccccc23)C1) `ZINC001721335106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721335106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721335106 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)Cc2cnn3ccccc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 24, 50, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 24, 24, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 316) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)Cc2cnn3ccccc23)C1) `ZINC001721335106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721335106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721335106 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)Cc2cnn3ccccc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 6, 6, 25, 50, 50, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 25, 25, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721335106 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335106 Building ZINC001721335112 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721335112 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/317 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn(C(C)(C)C(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001721335112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721335112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721335112 none Cc1cn(C(C)(C)C(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 28, 32, 32, 9, 28, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/318 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn(C(C)(C)C(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001721335112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721335112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721335112 none Cc1cn(C(C)(C)C(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 29, 32, 32, 7, 29, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721335112 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 Building ZINC001721335112 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721335112 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 317) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn(C(C)(C)C(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001721335112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721335112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721335112 none Cc1cn(C(C)(C)C(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 28, 32, 32, 9, 28, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 318) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn(C(C)(C)C(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001721335112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721335112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721335112 none Cc1cn(C(C)(C)C(=O)N2CC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 29, 32, 32, 7, 29, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721335112 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335112 Building ZINC001721335141 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721335141 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/319 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)COCc2cccnc2)C1) `ZINC001721335141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721335141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721335141 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 19, 24, 38, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 19, 38, 38, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/320 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)COCc2cccnc2)C1) `ZINC001721335141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721335141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721335141 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 15, 22, 37, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 15, 37, 37, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721335141 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 Building ZINC001721335141 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721335141 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 319) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)COCc2cccnc2)C1) `ZINC001721335141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721335141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721335141 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CN(C(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 19, 24, 38, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 19, 38, 38, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 320) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)COCc2cccnc2)C1) `ZINC001721335141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721335141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721335141 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CN(C(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 15, 22, 37, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 15, 37, 37, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721335141 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721335141 Building ZINC001721355033 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721355033 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/321 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(COCC(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001721355033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721355033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721355033 none Cc1cc(COCC(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 30, 15, 6, 6, 6, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 50, 49, 49, 15, 15, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/322 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(COCC(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001721355033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721355033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721355033 none Cc1cc(COCC(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 16, 8, 8, 8, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 8, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 173 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721355033 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 Building ZINC001721355033 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721355033 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 321) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(COCC(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001721355033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721355033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721355033 none Cc1cc(COCC(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 30, 15, 6, 6, 6, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 50, 49, 49, 15, 15, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 322) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(COCC(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001721355033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721355033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721355033 none Cc1cc(COCC(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 16, 8, 8, 8, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 8, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 173 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721355033 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721355033 Building ZINC001721357849 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721357849 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/323 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721357849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721357849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721357849 none CC(=O)NCC(C)(C)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 48, 26, 13, 26, 26, 13, 13, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 48, 48, 26, 26, 26, 26, 26, 26, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/324 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721357849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721357849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721357849 none CC(=O)NCC(C)(C)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 31, 20, 31, 31, 20, 20, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 49, 49, 31, 31, 31, 31, 31, 31, 20, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 206 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721357849 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 Building ZINC001721357849 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721357849 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 323) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721357849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721357849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721357849 none CC(=O)NCC(C)(C)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 48, 26, 13, 26, 26, 13, 13, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 48, 48, 26, 26, 26, 26, 26, 26, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 324) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721357849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721357849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721357849 none CC(=O)NCC(C)(C)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 31, 20, 31, 31, 20, 20, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 49, 49, 31, 31, 31, 31, 31, 31, 20, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 206 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721357849 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721357849 Building ZINC001721358747 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721358747 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/325 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCCC1) `ZINC001721358747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721358747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721358747 none CC(=O)NC1(C(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 24, 24, 24, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 48, 50, 50, 50, 50, 24, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/326 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCCC1) `ZINC001721358747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721358747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721358747 none CC(=O)NC1(C(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 32, 32, 32, 10, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 48, 48, 48, 48, 50, 50, 50, 50, 32, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721358747 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 Building ZINC001721358747 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721358747 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 325) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCCC1) `ZINC001721358747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721358747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721358747 none CC(=O)NC1(C(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 24, 24, 24, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 48, 50, 50, 50, 50, 24, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 326) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCCC1) `ZINC001721358747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721358747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721358747 none CC(=O)NC1(C(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 32, 32, 32, 10, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 48, 48, 48, 48, 50, 50, 50, 50, 32, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721358747 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721358747 Building ZINC001721360466 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721360466 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/327 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(CCC(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001721360466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721360466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721360466 none Cc1nccc(CCC(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 27, 8, 8, 8, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 50, 32, 32, 27, 27, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/328 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(CCC(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001721360466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721360466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721360466 none Cc1nccc(CCC(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 36, 15, 15, 15, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 39, 39, 36, 36, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 168 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721360466 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 Building ZINC001721360466 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721360466 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 327) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(CCC(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001721360466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721360466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721360466 none Cc1nccc(CCC(=O)NC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 27, 8, 8, 8, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 50, 32, 32, 27, 27, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 328) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(CCC(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001721360466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721360466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721360466 none Cc1nccc(CCC(=O)NC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 36, 15, 15, 15, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 39, 39, 36, 36, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 168 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721360466 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721360466 Building ZINC001721362571 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721362571 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/329 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001721362571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721362571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721362571 none CC(=O)N[C@@H](C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 9, 42, 9, 9, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 42, 49, 47, 50, 50, 50, 50, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/330 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001721362571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721362571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721362571 none CC(=O)N[C@@H](C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 46, 17, 46, 17, 17, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 46, 50, 46, 49, 49, 49, 49, 17, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721362571 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 Building ZINC001721362571 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721362571 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 329) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001721362571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721362571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721362571 none CC(=O)N[C@@H](C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 9, 42, 9, 9, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 42, 49, 47, 50, 50, 50, 50, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 330) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001721362571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721362571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721362571 none CC(=O)N[C@@H](C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 46, 17, 46, 17, 17, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 46, 50, 46, 49, 49, 49, 49, 17, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721362571 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721362571 Building ZINC001721371826 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721371826 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/331 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721371826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721371826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721371826 none C[C@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 12, 31, 31, 38, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 31, 31, 31, 38, 38, 50, 50, 50, 50, 50, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/332 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721371826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721371826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721371826 none C[C@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 22, 38, 38, 44, 50, 50, 50, 50, 50, 22, 22, 10, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 38, 38, 38, 44, 44, 50, 50, 50, 50, 50, 22, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721371826 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 Building ZINC001721371826 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721371826 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 331) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721371826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721371826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721371826 none C[C@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 12, 31, 31, 38, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 31, 31, 31, 38, 38, 50, 50, 50, 50, 50, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 332) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721371826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721371826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721371826 none C[C@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 22, 38, 38, 44, 50, 50, 50, 50, 50, 22, 22, 10, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 38, 38, 38, 44, 44, 50, 50, 50, 50, 50, 22, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721371826 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371826 Building ZINC001721371827 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721371827 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/333 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721371827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721371827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721371827 none C[C@@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 30, 30, 37, 50, 50, 50, 50, 50, 17, 17, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 37, 37, 50, 50, 50, 50, 50, 17, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/334 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721371827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721371827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721371827 none C[C@@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 24, 41, 41, 44, 50, 50, 50, 50, 50, 24, 24, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 41, 41, 41, 44, 44, 50, 50, 50, 50, 50, 24, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 175 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721371827 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 Building ZINC001721371827 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721371827 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 333) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721371827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721371827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721371827 none C[C@@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 30, 30, 37, 50, 50, 50, 50, 50, 17, 17, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 37, 37, 50, 50, 50, 50, 50, 17, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 334) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721371827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721371827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721371827 none C[C@@H](Cc1cnn(C)c1)C(=O)NC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 24, 41, 41, 44, 50, 50, 50, 50, 50, 24, 24, 9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 41, 41, 41, 44, 44, 50, 50, 50, 50, 50, 24, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 175 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721371827 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721371827 Building ZINC001721384964 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721384964 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/335 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721384964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721384964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721384964 none CCNC(=O)CCC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 28, 29, 21, 21, 21, 21, 8, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 29, 28, 28, 21, 21, 21, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/336 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721384964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721384964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721384964 none CCNC(=O)CCC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 27, 27, 27, 27, 13, 7, 7, 7, 3, 1, 4, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 31, 31, 27, 27, 27, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721384964 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 Building ZINC001721384964 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721384964 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 335) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721384964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721384964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721384964 none CCNC(=O)CCC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 28, 29, 21, 21, 21, 21, 8, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 29, 28, 28, 21, 21, 21, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 336) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721384964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721384964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721384964 none CCNC(=O)CCC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 27, 27, 27, 27, 13, 7, 7, 7, 3, 1, 4, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 31, 31, 27, 27, 27, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721384964 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721384964 Building ZINC001721385483 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385483 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/337 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721385483 none CCC[C@@H](NC(N)=O)C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 30, 35, 35, 49, 49, 49, 24, 30, 24, 24, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 24, 24, 24, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 267 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/338 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721385483 none CCC[C@@H](NC(N)=O)C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 32, 35, 35, 49, 49, 49, 26, 32, 26, 26, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385483 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 Building ZINC001721385483 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385483 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 337) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721385483 none CCC[C@@H](NC(N)=O)C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 30, 35, 35, 49, 49, 49, 24, 30, 24, 24, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 24, 24, 24, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 267 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 338) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721385483 none CCC[C@@H](NC(N)=O)C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 32, 35, 35, 49, 49, 49, 26, 32, 26, 26, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385483 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385483 Building ZINC001721385493 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385493 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/339 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(=O)c1) `ZINC001721385493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721385493 none Cc1ccn(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 20, 19, 20, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/340 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(=O)c1) `ZINC001721385493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721385493 none Cc1ccn(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 18, 18, 18, 18, 18, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385493 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 Building ZINC001721385493 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385493 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 339) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(=O)c1) `ZINC001721385493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721385493 none Cc1ccn(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 20, 19, 20, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 340) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(=O)c1) `ZINC001721385493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721385493 none Cc1ccn(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 18, 18, 18, 18, 18, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385493 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385493 Building ZINC001721385603 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385603 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/341 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)ncc1C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721385603 none COc1nc(C)ncc1C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 50, 50, 35, 33, 35, 33, 33, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/342 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)ncc1C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721385603 none COc1nc(C)ncc1C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 37, 33, 37, 33, 33, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385603 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 Building ZINC001721385603 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385603 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 341) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)ncc1C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721385603 none COc1nc(C)ncc1C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 50, 50, 35, 33, 35, 33, 33, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 342) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)ncc1C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721385603 none COc1nc(C)ncc1C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 37, 33, 37, 33, 33, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385603 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385603 Building ZINC001721385611 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385611 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/343 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2noc3c2COCC3)C1) `ZINC001721385611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721385611 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/344 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2noc3c2COCC3)C1) `ZINC001721385611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721385611 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 38, 50, 50, 50, 50, 50, 50, 50, 50, 42, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385611 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 Building ZINC001721385611 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385611 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 343) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2noc3c2COCC3)C1) `ZINC001721385611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721385611 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 344) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2noc3c2COCC3)C1) `ZINC001721385611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721385611 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 38, 50, 50, 50, 50, 50, 50, 50, 50, 42, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385611 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385611 Building ZINC001721385660 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385660 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/345 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@@H]1CC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721385660 none CN1C(=O)CC[C@@H]1CC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 39, 39, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/346 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@@H]1CC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721385660 none CN1C(=O)CC[C@@H]1CC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 22, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385660 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 Building ZINC001721385660 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385660 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 345) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@@H]1CC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721385660 none CN1C(=O)CC[C@@H]1CC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 39, 39, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 346) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@@H]1CC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721385660 none CN1C(=O)CC[C@@H]1CC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 22, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385660 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385660 Building ZINC001721385661 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385661 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/347 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1CC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721385661 none CN1C(=O)CC[C@H]1CC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 37, 37, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/348 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1CC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721385661 none CN1C(=O)CC[C@H]1CC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 20, 21, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385661 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 Building ZINC001721385661 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385661 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 347) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1CC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721385661 none CN1C(=O)CC[C@H]1CC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 37, 37, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 348) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1CC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721385661 none CN1C(=O)CC[C@H]1CC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 21, 20, 21, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385661 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385661 Building ZINC001721385713 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385713 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/349 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3[nH]nnc3c2)C1) `ZINC001721385713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721385713 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3[nH]nnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 34, 34, 34, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 50, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/350 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3[nH]nnc3c2)C1) `ZINC001721385713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721385713 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3[nH]nnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 31, 31, 31, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 31, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385713 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 Building ZINC001721385713 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385713 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 349) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3[nH]nnc3c2)C1) `ZINC001721385713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721385713 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3[nH]nnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 34, 34, 34, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 50, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 350) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3[nH]nnc3c2)C1) `ZINC001721385713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721385713 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3[nH]nnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 31, 31, 31, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 31, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385713 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385713 Building ZINC001721385727 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385727 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/351 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)COc2cccnc2)C1) `ZINC001721385727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721385727 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 15, 15, 15, 15, 15, 30, 43, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 30, 30, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/352 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)COc2cccnc2)C1) `ZINC001721385727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721385727 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 15, 15, 28, 42, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 28, 28, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385727 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 Building ZINC001721385727 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385727 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 351) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)COc2cccnc2)C1) `ZINC001721385727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721385727 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 15, 15, 15, 15, 15, 30, 43, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 30, 30, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 352) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)COc2cccnc2)C1) `ZINC001721385727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721385727 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 15, 15, 28, 42, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 28, 28, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385727 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385727 Building ZINC001721385790 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385790 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/353 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001721385790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721385790 none CCn1cc(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 24, 17, 17, 17, 17, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 30, 30, 50, 50, 50, 50, 50, 30, 24, 24, 17, 17, 17, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/354 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001721385790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721385790 none CCn1cc(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 26, 18, 18, 18, 18, 18, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 33, 33, 50, 50, 50, 50, 50, 33, 26, 26, 18, 18, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385790 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 Building ZINC001721385790 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385790 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 353) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001721385790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721385790 none CCn1cc(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 24, 17, 17, 17, 17, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 30, 30, 50, 50, 50, 50, 50, 30, 24, 24, 17, 17, 17, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 354) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001721385790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721385790 none CCn1cc(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 26, 18, 18, 18, 18, 18, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 33, 33, 50, 50, 50, 50, 50, 33, 26, 26, 18, 18, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385790 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385790 Building ZINC001721385835 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385835 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/355 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2ccc3nncn3c2)C1) `ZINC001721385835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721385835 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2ccc3nncn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 22, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 22, 22, 22, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/356 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2ccc3nncn3c2)C1) `ZINC001721385835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721385835 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2ccc3nncn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 20, 20, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385835 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 Building ZINC001721385835 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385835 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 355) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2ccc3nncn3c2)C1) `ZINC001721385835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721385835 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2ccc3nncn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 22, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 22, 22, 22, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 356) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2ccc3nncn3c2)C1) `ZINC001721385835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721385835 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2ccc3nncn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 20, 20, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385835 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385835 Building ZINC001721385862 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385862 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/357 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)CCc2ccncn2)C1) `ZINC001721385862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721385862 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)CCc2ccncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 25, 25, 25, 25, 25, 41, 41, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 25, 25, 25, 41, 41, 41, 41, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/358 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)CCc2ccncn2)C1) `ZINC001721385862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721385862 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)CCc2ccncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 19, 19, 19, 19, 19, 38, 38, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 38, 38, 38, 38, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385862 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 Building ZINC001721385862 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721385862 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 357) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)CCc2ccncn2)C1) `ZINC001721385862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721385862 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)CCc2ccncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 25, 25, 25, 25, 25, 41, 41, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 25, 25, 25, 41, 41, 41, 41, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 358) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)CCc2ccncn2)C1) `ZINC001721385862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721385862 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)CCc2ccncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 19, 19, 19, 19, 19, 38, 38, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 38, 38, 38, 38, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385862 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385862 Building ZINC001721385890 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721385890 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/359 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 21, 20, 21, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/360 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 21, 20, 21, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/361 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/361' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 20, 20, 20, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/362 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/362' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 20, 20, 20, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385890 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 Building ZINC001721385890 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721385890 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 359) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 21, 20, 21, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 360) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 21, 20, 21, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 361) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 20, 20, 20, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 362) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 20, 20, 20, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385890 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 Building ZINC001721385890 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721385890 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 359) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 21, 20, 21, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 360) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 21, 20, 21, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 361) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 20, 20, 20, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 362) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 20, 20, 20, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385890 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 Building ZINC001721385890 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721385890 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 359) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 21, 20, 21, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 360) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 21, 20, 21, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 361) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 20, 20, 20, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 362) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721385890.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721385890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721385890 none CCCN(C)CCC(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 37, 48, 37, 20, 20, 20, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 37, 37, 37, 37, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 45, 50, 51, 49, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721385890 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721385890 Building ZINC001721386010 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386010 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/363 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nc(C(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001721386010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721386010 none COCc1nc(C(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 36, 36, 33, 31, 33, 31, 31, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 36, 36, 50, 50, 50, 50, 50, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 36] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/364 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nc(C(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001721386010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721386010 none COCc1nc(C(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 27, 27, 27, 27, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 28, 28, 50, 50, 50, 50, 50, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 28] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386010 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 Building ZINC001721386010 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386010 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 363) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nc(C(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001721386010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721386010 none COCc1nc(C(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 36, 36, 33, 31, 33, 31, 31, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 36, 36, 50, 50, 50, 50, 50, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 36] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 364) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nc(C(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001721386010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721386010 none COCc1nc(C(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 27, 27, 27, 27, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 28, 28, 50, 50, 50, 50, 50, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 28] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386010 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386010 Building ZINC001721386026 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386026 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/365 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3n2CCC3)C1) `ZINC001721386026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721386026 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 37, 37, 37, 42, 42, 50, 50, 50, 50, 50, 50, 50, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 32, 37, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/366 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3n2CCC3)C1) `ZINC001721386026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721386026 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 40, 40, 40, 43, 43, 50, 50, 50, 50, 50, 50, 50, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 40, 40, 50, 50, 50, 50, 50, 50, 50, 40, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386026 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 Building ZINC001721386026 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386026 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 365) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3n2CCC3)C1) `ZINC001721386026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721386026 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 37, 37, 37, 42, 42, 50, 50, 50, 50, 50, 50, 50, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 32, 37, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 366) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3n2CCC3)C1) `ZINC001721386026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721386026 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 40, 40, 40, 43, 43, 50, 50, 50, 50, 50, 50, 50, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 40, 40, 50, 50, 50, 50, 50, 50, 50, 40, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386026 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386026 Building ZINC001721386064 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386064 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/367 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001721386064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721386064 none CCn1nc(C)c(C(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 27, 27, 26, 23, 26, 23, 23, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 27, 50, 50, 50, 50, 50, 27, 27, 27, 23, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/368 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001721386064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721386064 none CCn1nc(C)c(C(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 26, 24, 22, 24, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 26, 50, 50, 50, 50, 50, 26, 26, 26, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386064 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 Building ZINC001721386064 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386064 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 367) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001721386064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721386064 none CCn1nc(C)c(C(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 27, 27, 26, 23, 26, 23, 23, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 27, 50, 50, 50, 50, 50, 27, 27, 27, 23, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 368) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001721386064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721386064 none CCn1nc(C)c(C(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 26, 24, 22, 24, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 26, 50, 50, 50, 50, 50, 26, 26, 26, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386064 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386064 Building ZINC001721386156 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386156 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/369 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)C(C)(C)c2cnc[nH]2)C1) `ZINC001721386156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386156 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)C(C)(C)c2cnc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 37, 37, 37, 45, 45, 46, 46, 46, 50, 50, 50, 50, 50, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 37, 37, 37, 46, 46, 46, 46, 46, 46, 50, 50, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/370 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/370' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)C(C)(C)c2cnc[nH]2)C1) `ZINC001721386156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386156 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)C(C)(C)c2cnc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 35, 35, 35, 44, 44, 45, 45, 45, 50, 50, 50, 50, 50, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 35, 35, 35, 45, 45, 45, 45, 45, 45, 50, 50, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386156 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 Building ZINC001721386156 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386156 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 369) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)C(C)(C)c2cnc[nH]2)C1) `ZINC001721386156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386156 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)C(C)(C)c2cnc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 37, 37, 37, 45, 45, 46, 46, 46, 50, 50, 50, 50, 50, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 37, 37, 37, 46, 46, 46, 46, 46, 46, 50, 50, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 370) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)C(C)(C)c2cnc[nH]2)C1) `ZINC001721386156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386156 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)C(C)(C)c2cnc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 35, 35, 35, 44, 44, 45, 45, 45, 50, 50, 50, 50, 50, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 35, 35, 35, 45, 45, 45, 45, 45, 45, 50, 50, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386156 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386156 Building ZINC001721386177 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386177 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/371 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cn3c(n2)COCC3)C1) `ZINC001721386177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721386177 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cn3c(n2)COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 41, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/372 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cn3c(n2)COCC3)C1) `ZINC001721386177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721386177 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cn3c(n2)COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 40, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386177 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 Building ZINC001721386177 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386177 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 371) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cn3c(n2)COCC3)C1) `ZINC001721386177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721386177 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cn3c(n2)COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 41, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 372) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cn3c(n2)COCC3)C1) `ZINC001721386177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721386177 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)c2cn3c(n2)COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 40, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386177 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386177 Building ZINC001721386212 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386212 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/373 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@@H]2CCc3cncn3C2)C1) `ZINC001721386212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721386212 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@@H]2CCc3cncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 24, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/374 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@@H]2CCc3cncn3C2)C1) `ZINC001721386212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721386212 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@@H]2CCc3cncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 27, 27, 27, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386212 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 Building ZINC001721386212 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386212 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 373) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@@H]2CCc3cncn3C2)C1) `ZINC001721386212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721386212 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@@H]2CCc3cncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 24, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 374) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@@H]2CCc3cncn3C2)C1) `ZINC001721386212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721386212 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@@H]2CCc3cncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 27, 27, 27, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386212 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386212 Building ZINC001721386213 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386213 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/375 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@H]2CCc3cncn3C2)C1) `ZINC001721386213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721386213 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@H]2CCc3cncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 28, 30, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/376 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@H]2CCc3cncn3C2)C1) `ZINC001721386213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721386213 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@H]2CCc3cncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 27, 27, 27, 29, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386213 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 Building ZINC001721386213 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386213 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 375) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@H]2CCc3cncn3C2)C1) `ZINC001721386213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721386213 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@H]2CCc3cncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 28, 30, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 376) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@H]2CCc3cncn3C2)C1) `ZINC001721386213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721386213 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CN(C(=O)[C@H]2CCc3cncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 27, 27, 27, 29, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386213 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386213 Building ZINC001721386258 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386258 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/377 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nn(C)cc1C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721386258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386258 none CCc1nn(C)cc1C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 31, 31, 27, 27, 27, 27, 27, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 31, 31, 31, 31, 27, 27, 27, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/378 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nn(C)cc1C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721386258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386258 none CCc1nn(C)cc1C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25, 25, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 33, 33, 33, 33, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386258 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 Building ZINC001721386258 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386258 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 377) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nn(C)cc1C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721386258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386258 none CCc1nn(C)cc1C(=O)N1CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 31, 31, 27, 27, 27, 27, 27, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 31, 31, 31, 31, 27, 27, 27, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 378) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nn(C)cc1C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721386258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386258 none CCc1nn(C)cc1C(=O)N1CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25, 25, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 33, 33, 33, 33, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386258 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386258 Building ZINC001721386338 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386338 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/379 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001721386338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386338 none COc1ccc(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 20, 18, 20, 18, 18, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 45, 45, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/380 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001721386338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386338 none COc1ccc(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 19, 17, 19, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 46, 46, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386338 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 Building ZINC001721386338 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721386338 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 379) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001721386338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721386338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386338 none COc1ccc(CC(=O)N2CC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 20, 18, 20, 18, 18, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 45, 45, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 380) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001721386338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721386338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721386338 none COc1ccc(CC(=O)N2CC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 19, 17, 19, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 46, 46, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721386338 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721386338 Building ZINC001721395476 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721395476 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/381 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)Cn2cc(Cl)cn2)C1) `ZINC001721395476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721395476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721395476 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)Cn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 12, 23, 23, 23, 46, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 23, 46, 46, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/382 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)Cn2cc(Cl)cn2)C1) `ZINC001721395476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721395476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721395476 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)Cn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 13, 28, 28, 28, 47, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 13, 28, 47, 47, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 193 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721395476 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 Building ZINC001721395476 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721395476 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 381) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)Cn2cc(Cl)cn2)C1) `ZINC001721395476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721395476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721395476 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)Cn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 12, 23, 23, 23, 46, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 23, 46, 46, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 382) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)Cn2cc(Cl)cn2)C1) `ZINC001721395476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721395476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721395476 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)Cn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 13, 28, 28, 28, 47, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 13, 28, 47, 47, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 193 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721395476 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721395476 Building ZINC001721396053 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721396053 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/383 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721396053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721396053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721396053 none CCCS(=O)(=O)CC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 27, 27, 7, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/384 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/384' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721396053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721396053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721396053 none CCCS(=O)(=O)CC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 35, 35, 16, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721396053 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 Building ZINC001721396053 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721396053 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 383) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721396053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721396053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721396053 none CCCS(=O)(=O)CC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 27, 27, 7, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 384) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721396053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721396053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721396053 none CCCS(=O)(=O)CC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 35, 35, 16, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721396053 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396053 Building ZINC001721396359 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721396359 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/385 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCOCC(F)F)C1) `ZINC001721396359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721396359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721396359 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 12, 12, 12, 22, 22, 31, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 22, 22, 22, 22, 50, 50, 50, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/386 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCOCC(F)F)C1) `ZINC001721396359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721396359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721396359 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 9, 16, 16, 16, 27, 27, 32, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 16, 27, 27, 27, 27, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721396359 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 Building ZINC001721396359 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721396359 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 385) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCOCC(F)F)C1) `ZINC001721396359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721396359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721396359 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 12, 12, 12, 22, 22, 31, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 22, 22, 22, 22, 50, 50, 50, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 386) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCOCC(F)F)C1) `ZINC001721396359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721396359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721396359 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 9, 16, 16, 16, 27, 27, 32, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 16, 27, 27, 27, 27, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721396359 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721396359 Building ZINC001721398961 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721398961 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/387 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)C1CC1) `ZINC001721398961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721398961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721398961 none CN(CC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 20, 20, 20, 13, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 44, 46, 46, 50, 50, 44, 44, 44, 44, 44, 20, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/388 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)C1CC1) `ZINC001721398961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721398961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721398961 none CN(CC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 20, 20, 20, 10, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 37, 43, 43, 50, 50, 37, 37, 37, 36, 36, 20, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721398961 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 Building ZINC001721398961 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721398961 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 387) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)C1CC1) `ZINC001721398961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721398961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721398961 none CN(CC(=O)NCC1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 20, 20, 20, 13, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 44, 46, 46, 50, 50, 44, 44, 44, 44, 44, 20, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 388) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)C1CC1) `ZINC001721398961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721398961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721398961 none CN(CC(=O)NCC1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 20, 20, 20, 10, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 37, 43, 43, 50, 50, 37, 37, 37, 36, 36, 20, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721398961 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721398961 Building ZINC001721401845 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721401845 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/389 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCCn2ccnc2)C1) `ZINC001721401845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721401845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721401845 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 7, 16, 16, 16, 33, 26, 33, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 16, 33, 33, 33, 33, 33, 33, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/390 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCCn2ccnc2)C1) `ZINC001721401845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721401845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721401845 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 9, 15, 15, 15, 28, 21, 31, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 15, 28, 28, 28, 28, 30, 30, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721401845 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 Building ZINC001721401845 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721401845 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 389) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCCn2ccnc2)C1) `ZINC001721401845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721401845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721401845 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 7, 16, 16, 16, 33, 26, 33, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 16, 33, 33, 33, 33, 33, 33, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 390) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCCn2ccnc2)C1) `ZINC001721401845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721401845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721401845 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 9, 15, 15, 15, 28, 21, 31, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 15, 28, 28, 28, 28, 30, 30, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721401845 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721401845 Building ZINC001721402372 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721402372 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/391 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001721402372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721402372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721402372 none CC[C@]1(C(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 48, 22, 6, 6, 6, 3, 1, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/392 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001721402372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721402372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721402372 none CC[C@]1(C(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 10, 10, 10, 4, 1, 6, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721402372 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 Building ZINC001721402372 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721402372 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 391) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001721402372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721402372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721402372 none CC[C@]1(C(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 48, 22, 6, 6, 6, 3, 1, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 392) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001721402372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721402372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721402372 none CC[C@]1(C(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 10, 10, 10, 4, 1, 6, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721402372 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402372 Building ZINC001721402373 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721402373 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/393 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001721402373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721402373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721402373 none CC[C@@]1(C(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 46, 21, 6, 6, 6, 3, 1, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/394 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/394' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001721402373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721402373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721402373 none CC[C@@]1(C(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 29, 11, 11, 11, 4, 1, 6, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721402373 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 Building ZINC001721402373 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721402373 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 393) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001721402373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721402373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721402373 none CC[C@@]1(C(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 46, 21, 6, 6, 6, 3, 1, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 394) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001721402373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721402373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721402373 none CC[C@@]1(C(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 29, 11, 11, 11, 4, 1, 6, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721402373 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721402373 Building ZINC001721403516 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721403516 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/395 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@H]2CCCO2)C1) `ZINC001721403516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721403516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721403516 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 7, 17, 17, 17, 29, 44, 49, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 17, 29, 29, 49, 49, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/396 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@H]2CCCO2)C1) `ZINC001721403516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721403516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721403516 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 8, 20, 20, 20, 27, 43, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 20, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721403516 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 Building ZINC001721403516 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721403516 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 395) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@H]2CCCO2)C1) `ZINC001721403516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721403516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721403516 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 7, 17, 17, 17, 29, 44, 49, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 17, 29, 29, 49, 49, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 396) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@H]2CCCO2)C1) `ZINC001721403516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721403516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721403516 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 8, 20, 20, 20, 27, 43, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 20, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721403516 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403516 Building ZINC001721403517 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721403517 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/397 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@@H]2CCCO2)C1) `ZINC001721403517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721403517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721403517 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 9, 22, 22, 22, 33, 44, 48, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 22, 33, 33, 47, 47, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/398 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@@H]2CCCO2)C1) `ZINC001721403517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721403517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721403517 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 9, 18, 18, 18, 27, 43, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 18, 27, 27, 49, 49, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721403517 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 Building ZINC001721403517 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721403517 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 397) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@@H]2CCCO2)C1) `ZINC001721403517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721403517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721403517 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 9, 22, 22, 22, 33, 44, 48, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 22, 33, 33, 47, 47, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 398) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@@H]2CCCO2)C1) `ZINC001721403517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721403517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721403517 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COC[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 9, 18, 18, 18, 27, 43, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 18, 27, 27, 49, 49, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721403517 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721403517 Building ZINC001721407332 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721407332 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/399 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COCc2cccnc2)C1) `ZINC001721407332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721407332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721407332 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 18, 22, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 18, 18, 42, 42, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/400 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COCc2cccnc2)C1) `ZINC001721407332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721407332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721407332 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 8, 13, 13, 13, 15, 18, 36, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 13, 15, 15, 36, 36, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721407332 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 Building ZINC001721407332 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721407332 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 399) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COCc2cccnc2)C1) `ZINC001721407332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721407332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721407332 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 18, 22, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 18, 18, 42, 42, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 400) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COCc2cccnc2)C1) `ZINC001721407332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721407332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721407332 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 8, 13, 13, 13, 15, 18, 36, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 13, 15, 15, 36, 36, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721407332 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721407332 Building ZINC001721411712 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721411712 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/401 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 12, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/402 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 12, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/403 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/403' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 20, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/404 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/404' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 18, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721411712 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 Building ZINC001721411712 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721411712 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 401) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 12, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 402) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 12, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 403) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 20, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 404) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 18, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721411712 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 Building ZINC001721411712 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721411712 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 401) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 12, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 402) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 12, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 403) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 20, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 404) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 18, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721411712 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 Building ZINC001721411712 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721411712 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 401) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 12, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 402) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 12, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 403) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 20, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 404) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001721411712.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721411712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721411712 none C[C@H]1CC[N@@](CC(=O)NCC2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 34, 34, 18, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721411712 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721411712 Building ZINC001721422894 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721422894 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/405 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CC(=O)NCC1CC1) `ZINC001721422894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721422894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721422894 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CC(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 28, 28, 28, 44, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 28, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/406 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CC(=O)NCC1CC1) `ZINC001721422894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721422894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721422894 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CC(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 41, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721422894 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 Building ZINC001721422894 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721422894 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 405) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CC(=O)NCC1CC1) `ZINC001721422894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721422894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721422894 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CC(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 28, 28, 28, 44, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 28, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 406) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CC(=O)NCC1CC1) `ZINC001721422894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721422894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721422894 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CC(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 41, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721422894 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422894 Building ZINC001721422997 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721422997 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/407 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721422997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721422997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721422997 none CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 22, 12, 22, 22, 6, 12, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 35, 22, 22, 22, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/408 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721422997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721422997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721422997 none CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 25, 13, 25, 25, 5, 13, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 25, 25, 25, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721422997 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 Building ZINC001721422997 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721422997 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 407) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721422997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721422997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721422997 none CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 22, 12, 22, 22, 6, 12, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 35, 22, 22, 22, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 408) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721422997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721422997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721422997 none CCC(=O)N[C@@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 25, 13, 25, 25, 5, 13, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 25, 25, 25, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721422997 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422997 Building ZINC001721422998 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721422998 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/409 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721422998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721422998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721422998 none CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 28, 12, 28, 28, 6, 12, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 28, 28, 28, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 222 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/410 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721422998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721422998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721422998 none CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 29, 11, 29, 29, 5, 11, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 37, 29, 29, 29, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721422998 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 Building ZINC001721422998 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721422998 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 409) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721422998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721422998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721422998 none CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 28, 12, 28, 28, 6, 12, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 28, 28, 28, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 222 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 410) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721422998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721422998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721422998 none CCC(=O)N[C@H](C)C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 29, 11, 29, 29, 5, 11, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 37, 29, 29, 29, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721422998 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721422998 Building ZINC001721423214 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721423214 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/411 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC1(C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721423214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721423214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721423214 none CN(C)CC1(C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 27, 8, 27, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 38, 38, 38, 38] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/412 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC1(C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721423214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721423214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721423214 none CN(C)CC1(C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 28, 8, 28, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721423214 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 Building ZINC001721423214 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721423214 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 411) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC1(C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721423214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721423214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721423214 none CN(C)CC1(C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 27, 8, 27, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 38, 38, 38, 38] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 412) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC1(C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721423214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721423214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721423214 none CN(C)CC1(C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 28, 8, 28, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721423214 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721423214 Building ZINC001721430826 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721430826 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/413 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N(CC)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721430826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721430826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721430826 none CCC(=O)NCC(=O)N(CC)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 25, 25, 26, 19, 13, 7, 13, 2, 7, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 48, 48, 48, 48, 48, 26, 19, 19, 8, 8, 8, 8, 8, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/414 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N(CC)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721430826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721430826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721430826 none CCC(=O)NCC(=O)N(CC)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 28, 29, 23, 16, 9, 16, 4, 9, 9, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 49, 49, 49, 49, 49, 29, 23, 23, 9, 9, 9, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721430826 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 Building ZINC001721430826 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721430826 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 413) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N(CC)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721430826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721430826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721430826 none CCC(=O)NCC(=O)N(CC)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 25, 25, 26, 19, 13, 7, 13, 2, 7, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 48, 48, 48, 48, 48, 26, 19, 19, 8, 8, 8, 8, 8, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 414) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N(CC)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721430826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721430826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721430826 none CCC(=O)NCC(=O)N(CC)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 28, 29, 23, 16, 9, 16, 4, 9, 9, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 49, 49, 49, 49, 49, 29, 23, 23, 9, 9, 9, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721430826 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430826 Building ZINC001721430827 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721430827 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/415 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N(CC)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721430827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721430827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721430827 none CCC(=O)NCC(=O)N(CC)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 29, 29, 30, 23, 15, 8, 15, 4, 8, 8, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 49, 49, 49, 49, 49, 30, 23, 23, 8, 8, 8, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/416 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N(CC)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721430827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721430827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721430827 none CCC(=O)NCC(=O)N(CC)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 25, 25, 26, 19, 13, 7, 13, 2, 7, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 48, 48, 48, 48, 48, 26, 19, 19, 8, 8, 8, 8, 8, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721430827 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 Building ZINC001721430827 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721430827 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 415) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N(CC)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721430827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721430827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721430827 none CCC(=O)NCC(=O)N(CC)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 29, 29, 30, 23, 15, 8, 15, 4, 8, 8, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 49, 49, 49, 49, 49, 30, 23, 23, 8, 8, 8, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 416) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N(CC)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721430827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721430827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721430827 none CCC(=O)NCC(=O)N(CC)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 25, 25, 26, 19, 13, 7, 13, 2, 7, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 48, 48, 48, 48, 48, 26, 19, 19, 8, 8, 8, 8, 8, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721430827 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721430827 Building ZINC001721431176 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431176 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/417 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COCCOC)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721431176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721431176 none CCN(C(=O)COCCOC)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 8, 8, 22, 41, 46, 50, 50, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 22, 22, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/418 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COCCOC)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721431176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721431176 none CCN(C(=O)COCCOC)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 9, 9, 21, 39, 46, 50, 50, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 21, 21, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431176 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 Building ZINC001721431176 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431176 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 417) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COCCOC)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721431176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721431176 none CCN(C(=O)COCCOC)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 8, 8, 22, 41, 46, 50, 50, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 22, 22, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 418) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COCCOC)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721431176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721431176 none CCN(C(=O)COCCOC)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 9, 9, 21, 39, 46, 50, 50, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 21, 21, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431176 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431176 Building ZINC001721431177 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431177 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/419 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COCCOC)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721431177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721431177 none CCN(C(=O)COCCOC)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 9, 9, 21, 39, 46, 50, 50, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 21, 21, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/420 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COCCOC)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721431177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721431177 none CCN(C(=O)COCCOC)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 8, 8, 22, 41, 46, 50, 50, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 22, 22, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431177 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 Building ZINC001721431177 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431177 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 419) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COCCOC)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721431177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721431177 none CCN(C(=O)COCCOC)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 9, 9, 21, 39, 46, 50, 50, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 21, 21, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 420) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COCCOC)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721431177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721431177 none CCN(C(=O)COCCOC)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 8, 8, 22, 41, 46, 50, 50, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 22, 22, 46, 46, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431177 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431177 Building ZINC001721431582 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431582 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/421 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCNC(N)=O)C1) `ZINC001721431582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721431582 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 12, 12, 35, 36, 45, 45, 45, 9, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 35, 36, 36, 45, 45, 45, 9, 9] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/422 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCNC(N)=O)C1) `ZINC001721431582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721431582 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 15, 15, 38, 39, 50, 50, 50, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 38, 38, 39, 39, 50, 50, 50, 11, 11] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431582 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 Building ZINC001721431582 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431582 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 421) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCNC(N)=O)C1) `ZINC001721431582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721431582 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 12, 12, 35, 36, 45, 45, 45, 9, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 35, 36, 36, 45, 45, 45, 9, 9] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 422) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCNC(N)=O)C1) `ZINC001721431582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721431582 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 15, 15, 38, 39, 50, 50, 50, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 38, 38, 39, 39, 50, 50, 50, 11, 11] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431582 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431582 Building ZINC001721431583 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431583 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/423 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCNC(N)=O)C1) `ZINC001721431583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721431583 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 10, 10, 17, 17, 40, 40, 50, 50, 50, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 40, 40, 40, 40, 50, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/424 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/424' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCNC(N)=O)C1) `ZINC001721431583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721431583 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 12, 12, 35, 36, 43, 43, 43, 9, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 35, 36, 36, 43, 43, 43, 9, 9] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431583 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 Building ZINC001721431583 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431583 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 423) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCNC(N)=O)C1) `ZINC001721431583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721431583 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 10, 10, 17, 17, 40, 40, 50, 50, 50, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 40, 40, 40, 40, 50, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 424) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCNC(N)=O)C1) `ZINC001721431583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721431583 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 12, 12, 35, 36, 43, 43, 43, 9, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 35, 36, 36, 43, 43, 43, 9, 9] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431583 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431583 Building ZINC001721431694 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431694 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/425 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1) `ZINC001721431694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431694 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 27, 32, 46, 46, 46, 46, 46, 46, 15, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 46, 46, 46, 46, 46, 15, 15] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/426 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1) `ZINC001721431694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431694 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 28, 30, 50, 50, 50, 50, 50, 50, 16, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431694 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 Building ZINC001721431694 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431694 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 425) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1) `ZINC001721431694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431694 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 27, 32, 46, 46, 46, 46, 46, 46, 15, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 46, 46, 46, 46, 46, 15, 15] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 426) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1) `ZINC001721431694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431694 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 28, 30, 50, 50, 50, 50, 50, 50, 16, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431694 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431694 Building ZINC001721431695 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431695 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/427 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1) `ZINC001721431695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431695 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 25, 30, 50, 50, 50, 50, 50, 50, 15, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/428 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/428' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1) `ZINC001721431695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431695 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 18, 28, 32, 47, 47, 47, 47, 47, 47, 18, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 47, 47, 47, 47, 47, 18, 18] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431695 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 Building ZINC001721431695 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431695 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 427) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1) `ZINC001721431695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431695 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 25, 30, 50, 50, 50, 50, 50, 50, 15, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 428) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1) `ZINC001721431695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431695 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 18, 28, 32, 47, 47, 47, 47, 47, 47, 18, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 47, 47, 47, 47, 47, 18, 18] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431695 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431695 Building ZINC001721431696 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431696 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/429 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1) `ZINC001721431696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431696 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 29, 30, 47, 47, 47, 47, 47, 47, 16, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 47, 47, 47, 47, 47, 16, 16] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/430 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1) `ZINC001721431696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431696 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 16, 16, 16, 16, 16, 26, 27, 45, 45, 45, 45, 45, 45, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 45, 45, 45, 45, 45, 16, 16] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431696 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 Building ZINC001721431696 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431696 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 429) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1) `ZINC001721431696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431696 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 29, 30, 47, 47, 47, 47, 47, 47, 16, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 47, 47, 47, 47, 47, 16, 16] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 430) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1) `ZINC001721431696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431696 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 16, 16, 16, 16, 16, 26, 27, 45, 45, 45, 45, 45, 45, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 45, 45, 45, 45, 45, 16, 16] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431696 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431696 Building ZINC001721431697 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431697 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/431 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1) `ZINC001721431697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431697 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 25, 26, 45, 45, 45, 45, 45, 45, 13, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 45, 45, 45, 45, 45, 13, 13] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/432 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/432' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1) `ZINC001721431697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431697 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 28, 29, 47, 47, 47, 47, 47, 47, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 47, 47, 47, 47, 47, 16, 16] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431697 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 Building ZINC001721431697 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431697 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 431) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1) `ZINC001721431697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431697 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 25, 26, 45, 45, 45, 45, 45, 45, 13, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 45, 45, 45, 45, 45, 13, 13] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 432) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1) `ZINC001721431697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721431697 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 28, 29, 47, 47, 47, 47, 47, 47, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 47, 47, 47, 47, 47, 16, 16] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431697 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431697 Building ZINC001721431978 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431978 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/433 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CS(C)(=O)=O)C1) `ZINC001721431978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721431978 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 9, 9, 30, 46, 46, 46, 6, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 30, 30, 46, 46, 46, 6, 6] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 35, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/434 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CS(C)(=O)=O)C1) `ZINC001721431978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721431978 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 12, 12, 36, 50, 50, 50, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 36, 36, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 35, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431978 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 Building ZINC001721431978 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431978 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 433) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CS(C)(=O)=O)C1) `ZINC001721431978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721431978 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 9, 9, 30, 46, 46, 46, 6, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 30, 30, 46, 46, 46, 6, 6] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 35, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 434) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CS(C)(=O)=O)C1) `ZINC001721431978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721431978 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 12, 12, 36, 50, 50, 50, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 36, 36, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 35, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431978 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431978 Building ZINC001721431979 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431979 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/435 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CS(C)(=O)=O)C1) `ZINC001721431979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721431979 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 11, 11, 36, 50, 50, 50, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 36, 36, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 35, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 210 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/436 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CS(C)(=O)=O)C1) `ZINC001721431979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721431979 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 9, 9, 30, 46, 46, 46, 6, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 30, 30, 46, 46, 46, 6, 6] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 35, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431979 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 Building ZINC001721431979 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721431979 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 435) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CS(C)(=O)=O)C1) `ZINC001721431979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721431979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721431979 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 11, 11, 36, 50, 50, 50, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 36, 36, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 35, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 210 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 436) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CS(C)(=O)=O)C1) `ZINC001721431979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721431979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721431979 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 9, 9, 30, 46, 46, 46, 6, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 30, 30, 46, 46, 46, 6, 6] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 35, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721431979 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721431979 Building ZINC001721432056 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432056 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/437 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)Cn2nccn2)C1) `ZINC001721432056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721432056 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)Cn2nccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 12, 12, 39, 48, 48, 48, 48, 7, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 39, 39, 48, 48, 7, 7] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/438 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/438' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)Cn2nccn2)C1) `ZINC001721432056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721432056 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)Cn2nccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 11, 11, 41, 50, 50, 50, 50, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 41, 41, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432056 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 Building ZINC001721432056 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432056 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 437) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)Cn2nccn2)C1) `ZINC001721432056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721432056 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)Cn2nccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 12, 12, 39, 48, 48, 48, 48, 7, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 39, 39, 48, 48, 7, 7] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 438) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)Cn2nccn2)C1) `ZINC001721432056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721432056 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)Cn2nccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 11, 11, 41, 50, 50, 50, 50, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 41, 41, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432056 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432056 Building ZINC001721432057 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432057 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/439 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)Cn2nccn2)C1) `ZINC001721432057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721432057 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)Cn2nccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 10, 10, 39, 50, 50, 50, 50, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 39, 39, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/440 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)Cn2nccn2)C1) `ZINC001721432057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721432057 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)Cn2nccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 13, 13, 40, 47, 47, 47, 47, 7, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 40, 40, 47, 47, 7, 7] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 170 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432057 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 Building ZINC001721432057 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432057 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 439) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)Cn2nccn2)C1) `ZINC001721432057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721432057 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)Cn2nccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 10, 10, 39, 50, 50, 50, 50, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 39, 39, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 440) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)Cn2nccn2)C1) `ZINC001721432057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721432057 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)Cn2nccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 13, 13, 40, 47, 47, 47, 47, 7, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 40, 40, 47, 47, 7, 7] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 170 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432057 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432057 Building ZINC001721432715 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432715 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/441 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1) `ZINC001721432715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432715 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 26, 34, 44, 44, 44, 44, 44, 44, 13, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 44, 44, 44, 44, 44, 13, 13] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/442 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/442' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1) `ZINC001721432715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432715 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 28, 37, 50, 50, 50, 50, 50, 50, 17, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432715 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 Building ZINC001721432715 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432715 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 441) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1) `ZINC001721432715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432715 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 26, 34, 44, 44, 44, 44, 44, 44, 13, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 44, 44, 44, 44, 44, 13, 13] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 442) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1) `ZINC001721432715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432715 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 28, 37, 50, 50, 50, 50, 50, 50, 17, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432715 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432715 Building ZINC001721432717 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432717 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/443 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1) `ZINC001721432717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432717 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 15, 29, 36, 50, 50, 50, 50, 50, 50, 15, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/444 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1) `ZINC001721432717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432717 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 27, 34, 44, 44, 44, 44, 44, 44, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 44, 44, 44, 44, 44, 16, 16] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 134 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432717 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 Building ZINC001721432717 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432717 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 443) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1) `ZINC001721432717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432717 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 15, 29, 36, 50, 50, 50, 50, 50, 50, 15, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 444) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1) `ZINC001721432717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432717 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 27, 34, 44, 44, 44, 44, 44, 44, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 44, 44, 44, 44, 44, 16, 16] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 134 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432717 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432717 Building ZINC001721432719 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432719 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/445 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1) `ZINC001721432719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432719 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 29, 34, 50, 50, 50, 50, 50, 50, 13, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/446 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/446' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1) `ZINC001721432719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432719 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 27, 31, 45, 45, 45, 45, 45, 45, 13, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 45, 45, 45, 45, 45, 13, 13] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432719 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 Building ZINC001721432719 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432719 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 445) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1) `ZINC001721432719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432719 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 29, 34, 50, 50, 50, 50, 50, 50, 13, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 446) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1) `ZINC001721432719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432719 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 27, 31, 45, 45, 45, 45, 45, 45, 13, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 45, 45, 45, 45, 45, 13, 13] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432719 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432719 Building ZINC001721432721 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432721 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/447 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1) `ZINC001721432721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432721 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 27, 32, 45, 45, 45, 45, 45, 45, 13, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 45, 45, 45, 45, 45, 13, 13] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/448 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/448' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1) `ZINC001721432721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432721 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 29, 31, 50, 50, 50, 50, 50, 50, 15, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432721 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 Building ZINC001721432721 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721432721 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 447) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1) `ZINC001721432721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721432721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432721 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 27, 32, 45, 45, 45, 45, 45, 45, 13, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 45, 45, 45, 45, 45, 13, 13] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 448) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1) `ZINC001721432721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721432721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721432721 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 29, 31, 50, 50, 50, 50, 50, 50, 15, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 39, 35, 38, 37, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721432721 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721432721 Building ZINC001721436880 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721436880 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/449 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCn1ccnn1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721436880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721436880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721436880 none CCN(C(=O)CCn1ccnn1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 4, 10, 21, 21, 35, 42, 49, 49, 49, 49, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 35, 35, 42, 42, 49, 49, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/450 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/450' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCn1ccnn1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721436880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721436880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721436880 none CCN(C(=O)CCn1ccnn1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 4, 12, 24, 24, 33, 38, 49, 49, 49, 49, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 33, 33, 38, 38, 49, 49, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721436880 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 Building ZINC001721436880 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721436880 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 449) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCn1ccnn1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721436880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721436880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721436880 none CCN(C(=O)CCn1ccnn1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 4, 10, 21, 21, 35, 42, 49, 49, 49, 49, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 35, 35, 42, 42, 49, 49, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 450) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCn1ccnn1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721436880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721436880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721436880 none CCN(C(=O)CCn1ccnn1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 4, 12, 24, 24, 33, 38, 49, 49, 49, 49, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 33, 33, 38, 38, 49, 49, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721436880 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436880 Building ZINC001721436881 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721436881 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/451 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCn1ccnn1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721436881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721436881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721436881 none CCN(C(=O)CCn1ccnn1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 4, 12, 25, 25, 34, 39, 49, 49, 49, 49, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 34, 34, 39, 39, 49, 49, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/452 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/452' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCn1ccnn1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721436881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721436881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721436881 none CCN(C(=O)CCn1ccnn1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 5, 11, 21, 21, 35, 41, 49, 49, 49, 49, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 35, 35, 41, 41, 49, 49, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 178 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721436881 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 Building ZINC001721436881 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721436881 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 451) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCn1ccnn1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721436881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721436881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721436881 none CCN(C(=O)CCn1ccnn1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 4, 12, 25, 25, 34, 39, 49, 49, 49, 49, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 34, 34, 39, 39, 49, 49, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 452) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCn1ccnn1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001721436881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721436881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721436881 none CCN(C(=O)CCn1ccnn1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 5, 11, 21, 21, 35, 41, 49, 49, 49, 49, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 35, 35, 41, 41, 49, 49, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 178 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721436881 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721436881 Building ZINC001721456656 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456656 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/453 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C) `ZINC001721456656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721456656 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 9, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 34, 34, 42, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/454 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C) `ZINC001721456656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721456656 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 23, 11, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 31, 31, 43, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456656 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 Building ZINC001721456656 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456656 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 453) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C) `ZINC001721456656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721456656 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 9, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 34, 34, 42, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 454) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C) `ZINC001721456656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721456656 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 23, 11, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 31, 31, 43, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456656 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456656 Building ZINC001721456657 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456657 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/455 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C) `ZINC001721456657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721456657 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 10, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 34, 34, 40, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/456 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/456' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C) `ZINC001721456657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721456657 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 30, 30, 37, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456657 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 Building ZINC001721456657 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456657 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 455) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C) `ZINC001721456657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721456657 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 10, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 34, 34, 40, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 456) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C) `ZINC001721456657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721456657 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1OCCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 30, 30, 37, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456657 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456657 Building ZINC001721456878 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456878 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/457 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O) `ZINC001721456878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456878 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 41, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/458 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/458' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O) `ZINC001721456878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456878 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 33, 33, 45, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456878 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 Building ZINC001721456878 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456878 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 457) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O) `ZINC001721456878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456878 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 41, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 458) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O) `ZINC001721456878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456878 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 33, 33, 45, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456878 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456878 Building ZINC001721456879 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456879 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/459 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O) `ZINC001721456879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456879 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 44, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/460 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O) `ZINC001721456879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456879 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 38, 38, 45, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456879 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 Building ZINC001721456879 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456879 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 459) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O) `ZINC001721456879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456879 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 44, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 460) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O) `ZINC001721456879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456879 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 38, 38, 45, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456879 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456879 Building ZINC001721456880 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456880 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/461 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O) `ZINC001721456880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456880 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 32, 32, 46, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/462 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/462' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O) `ZINC001721456880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456880 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 41, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456880 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 Building ZINC001721456880 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456880 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 461) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O) `ZINC001721456880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456880 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 32, 32, 46, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 462) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O) `ZINC001721456880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456880 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 41, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456880 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456880 Building ZINC001721456881 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456881 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/463 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O) `ZINC001721456881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456881 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 36, 44, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/464 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O) `ZINC001721456881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456881 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 42, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456881 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 Building ZINC001721456881 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721456881 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 463) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O) `ZINC001721456881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721456881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456881 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 36, 44, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 464) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O) `ZINC001721456881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721456881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721456881 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 42, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721456881 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721456881 Building ZINC001721457820 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457820 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/465 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 11, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/466 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/466' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/467 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/467' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 11, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/468 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/468' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457820 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 Building ZINC001721457820 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457820 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 465) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 11, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 466) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 467) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 11, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 468) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457820 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 Building ZINC001721457820 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457820 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 465) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 11, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 466) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 467) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 11, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 468) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457820 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 Building ZINC001721457820 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457820 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 465) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 11, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 466) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 467) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 11, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 468) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457820.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457820 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457820 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457820 Building ZINC001721457821 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457821 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/469 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/470 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/470' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 20, 20, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/471 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/471' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/472 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/472' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 20, 20, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457821 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 Building ZINC001721457821 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457821 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 469) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 470) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 20, 20, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 471) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 472) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 20, 20, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457821 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 Building ZINC001721457821 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457821 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 469) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 470) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 20, 20, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 471) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 472) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 20, 20, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457821 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 Building ZINC001721457821 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457821 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 469) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 470) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 20, 20, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 471) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 472) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457821.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457821 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 20, 20, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457821 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457821 Building ZINC001721457822 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457822 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/473 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/474 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/474' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/475 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/475' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/476 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/476' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457822 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 Building ZINC001721457822 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457822 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 473) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 474) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 475) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 476) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457822 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 Building ZINC001721457822 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457822 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 473) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 474) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 475) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 476) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457822 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 Building ZINC001721457822 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457822 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 473) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 474) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 475) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 476) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC) `ZINC001721457822.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457822 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457822 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457822 Building ZINC001721457823 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457823 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/477 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 38, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/478 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 10, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 39, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/479 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/479' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 38, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/480 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/480' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 10, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 39, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457823 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 Building ZINC001721457823 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457823 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 477) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 38, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 478) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 10, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 39, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 479) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 38, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 480) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 10, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 39, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457823 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 Building ZINC001721457823 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457823 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 477) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 38, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 478) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 10, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 39, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 479) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 38, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 480) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 10, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 39, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457823 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 Building ZINC001721457823 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721457823 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 477) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 38, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 478) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 10, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 39, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 479) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 38, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 480) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC) `ZINC001721457823.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721457823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721457823 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1COCCN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 10, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 39, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457823 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457823 Building ZINC001721457856 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721457856 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/481 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1) `ZINC001721457856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721457856 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 28, 28, 37, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/482 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1) `ZINC001721457856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721457856 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 27, 27, 37, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457856 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 Building ZINC001721457856 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721457856 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 481) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1) `ZINC001721457856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721457856 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 28, 28, 37, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 482) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1) `ZINC001721457856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721457856 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 27, 27, 37, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457856 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457856 Building ZINC001721457857 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721457857 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/483 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1) `ZINC001721457857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721457857 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 26, 26, 40, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/484 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/484' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1) `ZINC001721457857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721457857 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 27, 27, 37, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457857 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 Building ZINC001721457857 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721457857 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 483) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1) `ZINC001721457857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721457857 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 26, 26, 40, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 484) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1) `ZINC001721457857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721457857 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 27, 27, 37, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457857 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457857 Building ZINC001721457906 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721457906 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/485 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1) `ZINC001721457906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721457906 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 19, 8, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/486 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/486' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1) `ZINC001721457906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721457906 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 11, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457906 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 Building ZINC001721457906 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721457906 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 485) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1) `ZINC001721457906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721457906 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 19, 8, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 486) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1) `ZINC001721457906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721457906 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 11, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457906 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457906 Building ZINC001721457907 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721457907 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/487 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1) `ZINC001721457907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721457907 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/488 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1) `ZINC001721457907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721457907 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 6, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457907 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 Building ZINC001721457907 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721457907 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 487) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1) `ZINC001721457907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721457907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721457907 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 488) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1) `ZINC001721457907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721457907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721457907 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 6, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721457907 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721457907 Building ZINC001721458080 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458080 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/489 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C) `ZINC001721458080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458080 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/490 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C) `ZINC001721458080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458080 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 48, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458080 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 Building ZINC001721458080 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458080 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 489) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C) `ZINC001721458080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458080 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 490) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C) `ZINC001721458080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458080 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 48, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458080 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458080 Building ZINC001721458081 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458081 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/491 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C) `ZINC001721458081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458081 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 48, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/492 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C) `ZINC001721458081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458081 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 45, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458081 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 Building ZINC001721458081 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458081 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 491) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C) `ZINC001721458081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458081 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 48, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 492) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C) `ZINC001721458081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458081 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 45, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458081 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458081 Building ZINC001721458082 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458082 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/493 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C) `ZINC001721458082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458082 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 18, 18, 18, 49, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/494 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C) `ZINC001721458082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458082 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 7, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458082 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 Building ZINC001721458082 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458082 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 493) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C) `ZINC001721458082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458082 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 18, 18, 18, 49, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 494) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C) `ZINC001721458082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458082 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 7, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458082 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458082 Building ZINC001721458083 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458083 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/495 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C) `ZINC001721458083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458083 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 7, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/496 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/496' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C) `ZINC001721458083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458083 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 18, 18, 18, 49, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458083 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 Building ZINC001721458083 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458083 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 495) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C) `ZINC001721458083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458083 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 7, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 496) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C) `ZINC001721458083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458083 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 18, 18, 18, 49, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458083 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458083 Building ZINC001721458480 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458480 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/497 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1) `ZINC001721458480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721458480 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 21, 21, 21, 39, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 39, 39, 50, 50, 100, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/498 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1) `ZINC001721458480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721458480 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 41, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 41, 41, 50, 50, 100, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458480 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 Building ZINC001721458480 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458480 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 497) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1) `ZINC001721458480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721458480 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 21, 21, 21, 39, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 39, 39, 50, 50, 100, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 498) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1) `ZINC001721458480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721458480 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 41, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 41, 41, 50, 50, 100, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458480 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458480 Building ZINC001721458481 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458481 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/499 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1) `ZINC001721458481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721458481 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 41, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 41, 41, 50, 50, 100, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/500 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1) `ZINC001721458481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721458481 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 23, 23, 23, 42, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 42, 42, 50, 50, 100, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 298 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458481 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 Building ZINC001721458481 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458481 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 499) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1) `ZINC001721458481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721458481 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 41, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 41, 41, 50, 50, 100, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 500) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1) `ZINC001721458481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721458481 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 23, 23, 23, 42, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 42, 42, 50, 50, 100, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 298 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458481 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458481 Building ZINC001721458640 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458640 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/501 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1) `ZINC001721458640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721458640 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 39, 39, 39, 48, 48, 48, 48, 48, 50, 48, 34, 34, 34, 34, 34, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 48, 48, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/502 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/502' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1) `ZINC001721458640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721458640 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 9, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 37, 48, 48, 48, 48, 48, 50, 48, 32, 32, 32, 32, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 48, 48, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458640 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 Building ZINC001721458640 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458640 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 501) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1) `ZINC001721458640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721458640 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 14, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 39, 39, 39, 48, 48, 48, 48, 48, 50, 48, 34, 34, 34, 34, 34, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 48, 48, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 502) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1) `ZINC001721458640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721458640 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 9, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 37, 48, 48, 48, 48, 48, 50, 48, 32, 32, 32, 32, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 48, 48, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458640 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458640 Building ZINC001721458641 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458641 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/503 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1) `ZINC001721458641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721458641 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 9, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 37, 48, 48, 48, 48, 48, 50, 48, 32, 32, 32, 32, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 48, 48, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/504 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1) `ZINC001721458641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721458641 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 49, 49, 49, 49, 49, 50, 49, 34, 34, 34, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 49, 49, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458641 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 Building ZINC001721458641 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458641 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 503) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1) `ZINC001721458641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721458641 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 9, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 37, 48, 48, 48, 48, 48, 50, 48, 32, 32, 32, 32, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 48, 48, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 504) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1) `ZINC001721458641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721458641 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 49, 49, 49, 49, 49, 50, 49, 34, 34, 34, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 49, 49, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458641 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458641 Building ZINC001721458642 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458642 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/505 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001721458642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458642 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 24, 36, 36, 36, 36, 36, 36, 50, 36, 14, 14, 14, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 36, 36, 50, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/506 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001721458642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458642 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 7, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 18, 18, 23, 36, 36, 36, 36, 36, 36, 50, 36, 16, 16, 16, 16, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 36, 36, 50, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458642 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 Building ZINC001721458642 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458642 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 505) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001721458642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458642 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 24, 36, 36, 36, 36, 36, 36, 50, 36, 14, 14, 14, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 36, 36, 50, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 506) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001721458642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458642 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 7, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 18, 18, 23, 36, 36, 36, 36, 36, 36, 50, 36, 16, 16, 16, 16, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 36, 36, 50, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458642 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458642 Building ZINC001721458643 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458643 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/507 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001721458643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458643 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 7, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 17, 17, 22, 34, 34, 34, 34, 34, 34, 50, 34, 16, 16, 16, 16, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 34, 34, 50, 50, 50, 50, 50, 34, 34] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/508 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001721458643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458643 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 16, 16, 25, 38, 38, 38, 38, 38, 38, 50, 38, 11, 11, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 38, 38, 50, 50, 50, 50, 50, 38, 38] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458643 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 Building ZINC001721458643 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458643 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 507) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001721458643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458643 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 7, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 17, 17, 22, 34, 34, 34, 34, 34, 34, 50, 34, 16, 16, 16, 16, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 34, 34, 50, 50, 50, 50, 50, 34, 34] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 508) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001721458643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458643 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 16, 16, 25, 38, 38, 38, 38, 38, 38, 50, 38, 11, 11, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 38, 38, 50, 50, 50, 50, 50, 38, 38] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458643 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458643 Building ZINC001721458644 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458644 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/509 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001721458644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458644 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 12, 12, 15, 30, 30, 30, 30, 30, 30, 50, 30, 9, 9, 9, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/510 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001721458644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458644 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 17, 32, 32, 32, 32, 32, 32, 50, 32, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 32, 32, 50, 50, 50, 50, 50, 32, 32] 50 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458644 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 Building ZINC001721458644 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458644 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 509) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001721458644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458644 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 12, 12, 15, 30, 30, 30, 30, 30, 30, 50, 30, 9, 9, 9, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 510) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1) `ZINC001721458644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458644 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 17, 32, 32, 32, 32, 32, 32, 50, 32, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 32, 32, 50, 50, 50, 50, 50, 32, 32] 50 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458644 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458644 Building ZINC001721458645 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458645 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/511 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001721458645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458645 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 17, 35, 35, 35, 35, 35, 35, 50, 35, 11, 11, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 35, 35, 50, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/512 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001721458645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458645 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 7, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 14, 14, 19, 38, 38, 38, 38, 38, 38, 50, 38, 10, 10, 10, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 38, 38, 50, 50, 50, 50, 50, 38, 38] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458645 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 Building ZINC001721458645 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721458645 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 511) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001721458645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721458645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458645 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 17, 35, 35, 35, 35, 35, 35, 50, 35, 11, 11, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 35, 35, 50, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 512) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1) `ZINC001721458645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721458645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721458645 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CC(=O)N(CC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 7, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 14, 14, 19, 38, 38, 38, 38, 38, 38, 50, 38, 10, 10, 10, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 38, 38, 50, 50, 50, 50, 50, 38, 38] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721458645 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721458645 Building ZINC001721470918 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721470918 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/513 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721470918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721470918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470918 none CC[C@@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 2, 7, 7, 20, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 20, 20, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/514 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721470918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721470918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470918 none CC[C@@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 2, 8, 8, 18, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721470918 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 Building ZINC001721470918 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721470918 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 513) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721470918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721470918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470918 none CC[C@@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 2, 7, 7, 20, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 20, 20, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 514) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721470918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721470918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470918 none CC[C@@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 2, 8, 8, 18, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721470918 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470918 Building ZINC001721470920 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721470920 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/515 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721470920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721470920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470920 none CC[C@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 16, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/516 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721470920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721470920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470920 none CC[C@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 2, 7, 7, 19, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 19, 19, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721470920 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 Building ZINC001721470920 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721470920 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 515) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721470920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721470920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470920 none CC[C@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 16, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 516) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721470920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721470920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470920 none CC[C@H](CNC(=O)[C@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 2, 7, 7, 19, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 19, 19, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721470920 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470920 Building ZINC001721470922 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721470922 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/517 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721470922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721470922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470922 none CC[C@@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 2, 7, 7, 19, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 19, 19, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/518 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721470922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721470922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470922 none CC[C@@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 16, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721470922 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 Building ZINC001721470922 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721470922 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 517) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721470922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721470922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470922 none CC[C@@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 2, 7, 7, 19, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 19, 19, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 518) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721470922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721470922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470922 none CC[C@@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 16, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721470922 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470922 Building ZINC001721470924 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721470924 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/519 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721470924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721470924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470924 none CC[C@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 2, 8, 8, 18, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/520 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721470924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721470924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470924 none CC[C@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 2, 7, 7, 19, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 19, 19, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 230 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721470924 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 Building ZINC001721470924 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721470924 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 519) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721470924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721470924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470924 none CC[C@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 2, 8, 8, 18, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 520) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721470924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721470924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721470924 none CC[C@H](CNC(=O)[C@@H]1CN2CCC1CC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 2, 7, 7, 19, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 19, 19, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 50, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 230 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721470924 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721470924 Building ZINC001721471964 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721471964 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/521 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721471964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721471964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721471964 none CC[C@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 5, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 15, 35, 35, 35, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 35, 44, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/522 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721471964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721471964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721471964 none CC[C@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 5, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 15, 26, 26, 26, 49, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 26, 49, 49, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721471964 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 Building ZINC001721471964 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721471964 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 521) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721471964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721471964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721471964 none CC[C@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 5, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 15, 35, 35, 35, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 35, 44, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 522) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721471964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721471964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721471964 none CC[C@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 5, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 15, 26, 26, 26, 49, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 26, 49, 49, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721471964 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471964 Building ZINC001721471965 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721471965 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/523 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721471965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721471965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721471965 none CC[C@@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 5, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 5, 5, 15, 25, 25, 25, 49, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 25, 49, 49, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/524 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721471965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721471965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721471965 none CC[C@@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 5, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 15, 35, 35, 35, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 35, 44, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721471965 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 Building ZINC001721471965 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721471965 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 523) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721471965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721471965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721471965 none CC[C@@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 5, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 5, 5, 15, 25, 25, 25, 49, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 25, 49, 49, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 524) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721471965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721471965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721471965 none CC[C@@H](CNC(=O)Cn1ccc(C)cc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 5, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 15, 35, 35, 35, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 35, 44, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721471965 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721471965 Building ZINC001721472412 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721472412 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/525 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721472412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721472412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472412 none CC[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 11, 20, 20, 20, 45, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 20, 45, 45, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/526 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721472412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721472412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472412 none CC[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 8, 14, 14, 14, 36, 47, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 14, 36, 36, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721472412 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 Building ZINC001721472412 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721472412 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 525) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721472412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721472412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472412 none CC[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 11, 20, 20, 20, 45, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 20, 45, 45, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 526) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721472412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721472412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472412 none CC[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 8, 14, 14, 14, 36, 47, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 14, 36, 36, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721472412 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472412 Building ZINC001721472413 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721472413 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/527 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721472413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721472413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472413 none CC[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 9, 15, 15, 15, 38, 48, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 15, 38, 38, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/528 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721472413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721472413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472413 none CC[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 11, 20, 20, 20, 45, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 20, 45, 45, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721472413 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 Building ZINC001721472413 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721472413 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 527) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721472413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721472413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472413 none CC[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 9, 15, 15, 15, 38, 48, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 15, 38, 38, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 528) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721472413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721472413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472413 none CC[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 11, 20, 20, 20, 45, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 20, 45, 45, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721472413 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472413 Building ZINC001721472414 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721472414 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/529 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721472414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721472414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472414 none CC[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 7, 10, 10, 10, 36, 48, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 10, 36, 36, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/530 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/530' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721472414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721472414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472414 none CC[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 10, 19, 19, 19, 44, 49, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 19, 44, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721472414 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 Building ZINC001721472414 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721472414 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 529) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721472414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721472414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472414 none CC[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 7, 10, 10, 10, 36, 48, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 10, 36, 36, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 530) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721472414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721472414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472414 none CC[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 10, 19, 19, 19, 44, 49, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 19, 44, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721472414 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472414 Building ZINC001721472415 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721472415 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/531 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721472415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721472415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472415 none CC[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 9, 17, 17, 17, 41, 47, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 17, 41, 41, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/532 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721472415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721472415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472415 none CC[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 7, 10, 10, 10, 37, 47, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 10, 37, 37, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721472415 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 Building ZINC001721472415 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721472415 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 531) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721472415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721472415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472415 none CC[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 9, 17, 17, 17, 41, 47, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 17, 41, 41, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 532) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721472415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721472415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721472415 none CC[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 7, 10, 10, 10, 37, 47, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 10, 37, 37, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721472415 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721472415 Building ZINC001721478714 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721478714 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/533 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721478714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721478714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721478714 none CC[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 2, 7, 7, 16, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 33, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/534 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/534' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721478714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721478714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721478714 none CC[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 2, 7, 7, 16, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 16, 16, 33, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721478714 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 Building ZINC001721478714 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721478714 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 533) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721478714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721478714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721478714 none CC[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 2, 7, 7, 16, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 33, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 534) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721478714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721478714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721478714 none CC[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 2, 7, 7, 16, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 16, 16, 33, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721478714 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478714 Building ZINC001721478715 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721478715 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/535 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721478715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721478715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721478715 none CC[C@@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 2, 7, 7, 16, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 16, 16, 33, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/536 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721478715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721478715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721478715 none CC[C@@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 2, 7, 7, 16, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 34, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721478715 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 Building ZINC001721478715 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721478715 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 535) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721478715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721478715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721478715 none CC[C@@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 2, 7, 7, 16, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 16, 16, 33, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 536) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721478715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721478715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721478715 none CC[C@@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 2, 7, 7, 16, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 34, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721478715 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721478715 Building ZINC001721482230 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721482230 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/537 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721482230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721482230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721482230 none CC[C@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 5, 15, 30, 30, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/538 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721482230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721482230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721482230 none CC[C@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 2, 6, 6, 15, 29, 29, 35, 49, 49, 49, 49, 49, 49, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 29, 49, 49, 49, 49, 49, 49, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721482230 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 Building ZINC001721482230 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721482230 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 537) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721482230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721482230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721482230 none CC[C@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 5, 15, 30, 30, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 538) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721482230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721482230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721482230 none CC[C@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 2, 6, 6, 15, 29, 29, 35, 49, 49, 49, 49, 49, 49, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 29, 49, 49, 49, 49, 49, 49, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721482230 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482230 Building ZINC001721482231 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721482231 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/539 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721482231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721482231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721482231 none CC[C@@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 14, 27, 27, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/540 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721482231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721482231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721482231 none CC[C@@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 17, 34, 34, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721482231 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 Building ZINC001721482231 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721482231 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 539) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721482231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721482231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721482231 none CC[C@@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 14, 27, 27, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 540) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721482231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721482231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721482231 none CC[C@@H](CNC(=O)[C@@H]1CCCN1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 17, 34, 34, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721482231 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482231 Building ZINC001721482660 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721482660 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/541 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721482660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721482660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721482660 none CC[C@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 5, 9, 13, 13, 13, 43, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 13, 39, 39, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/542 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721482660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721482660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721482660 none CC[C@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 5, 11, 11, 11, 37, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 11, 30, 30, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721482660 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 Building ZINC001721482660 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721482660 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 541) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721482660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721482660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721482660 none CC[C@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 5, 9, 13, 13, 13, 43, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 13, 39, 39, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 542) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721482660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721482660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721482660 none CC[C@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 5, 11, 11, 11, 37, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 11, 30, 30, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721482660 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482660 Building ZINC001721482661 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721482661 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/543 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721482661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721482661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721482661 none CC[C@@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 6, 11, 11, 11, 42, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 11, 32, 32, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/544 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/544' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721482661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721482661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721482661 none CC[C@@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 5, 8, 12, 12, 12, 40, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 12, 38, 38, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721482661 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 Building ZINC001721482661 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721482661 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 543) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721482661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721482661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721482661 none CC[C@@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 6, 11, 11, 11, 42, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 11, 32, 32, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 544) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721482661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721482661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721482661 none CC[C@@H](CNC(=O)CC1CS(=O)(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 5, 5, 8, 12, 12, 12, 40, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 12, 38, 38, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721482661 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721482661 Building ZINC001721485866 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721485866 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/545 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721485866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721485866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721485866 none CC[C@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 8, 18, 18, 18, 41, 41, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 18, 41, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/546 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721485866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721485866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721485866 none CC[C@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 10, 20, 20, 20, 41, 41, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 20, 41, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721485866 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 Building ZINC001721485866 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721485866 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 545) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721485866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721485866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721485866 none CC[C@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 8, 18, 18, 18, 41, 41, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 18, 41, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 546) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721485866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721485866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721485866 none CC[C@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 10, 20, 20, 20, 41, 41, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 20, 41, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721485866 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485866 Building ZINC001721485867 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721485867 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/547 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721485867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721485867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721485867 none CC[C@@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 9, 19, 19, 19, 38, 38, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 19, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/548 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721485867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721485867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721485867 none CC[C@@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 10, 21, 21, 21, 42, 42, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 21, 42, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721485867 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 Building ZINC001721485867 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721485867 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 547) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721485867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721485867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721485867 none CC[C@@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 9, 19, 19, 19, 38, 38, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 19, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 548) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721485867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721485867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721485867 none CC[C@@H](CNC(=O)CCN1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 10, 21, 21, 21, 42, 42, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 21, 42, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721485867 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721485867 Building ZINC001721507046 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721507046 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/549 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721507046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721507046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721507046 none CC[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 2, 7, 7, 16, 27, 27, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 27, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/550 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721507046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721507046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721507046 none CC[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 2, 7, 7, 16, 30, 30, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721507046 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 Building ZINC001721507046 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721507046 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 549) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721507046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721507046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721507046 none CC[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 2, 7, 7, 16, 27, 27, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 27, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 550) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721507046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721507046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721507046 none CC[C@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 2, 7, 7, 16, 30, 30, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721507046 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507046 Building ZINC001721507047 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721507047 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/551 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721507047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721507047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721507047 none CC[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 2, 6, 6, 15, 33, 33, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 178 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/552 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721507047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721507047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721507047 none CC[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 5, 14, 27, 27, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721507047 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 Building ZINC001721507047 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721507047 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 551) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721507047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721507047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721507047 none CC[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 2, 6, 6, 15, 33, 33, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 178 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 552) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721507047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721507047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721507047 none CC[C@@H](CNC(=O)[C@H]1CC[C@@H](C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 5, 14, 27, 27, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721507047 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721507047 Building ZINC001721515152 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515152 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/553 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721515152 none COCCOCC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 36, 22, 22, 22, 22, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 46, 46, 36, 36, 22, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/554 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721515152 none COCCOCC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 40, 34, 18, 18, 18, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 47, 47, 34, 34, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515152 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 Building ZINC001721515152 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515152 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 553) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721515152 none COCCOCC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 36, 22, 22, 22, 22, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 46, 46, 36, 36, 22, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 554) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721515152 none COCCOCC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 40, 34, 18, 18, 18, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 47, 47, 34, 34, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515152 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515152 Building ZINC001721515211 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515211 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/555 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515211 none CCNC(=O)CC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 26, 37, 12, 12, 12, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 37, 26, 26, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/556 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/556' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515211 none CCNC(=O)CC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 24, 36, 12, 12, 12, 4, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 36, 24, 24, 12, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515211 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 Building ZINC001721515211 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515211 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 555) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515211 none CCNC(=O)CC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 26, 37, 12, 12, 12, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 37, 26, 26, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 556) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515211 none CCNC(=O)CC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 24, 36, 12, 12, 12, 4, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 36, 24, 24, 12, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515211 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515211 Building ZINC001721515275 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515275 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/557 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC2)nnn1C) `ZINC001721515275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721515275 none Cc1c(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 36, 36, 18, 8, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 36, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/558 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC2)nnn1C) `ZINC001721515275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721515275 none Cc1c(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 15, 8, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 32, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515275 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 Building ZINC001721515275 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515275 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 557) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC2)nnn1C) `ZINC001721515275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721515275 none Cc1c(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 36, 36, 18, 8, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 36, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 558) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC2)nnn1C) `ZINC001721515275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721515275 none Cc1c(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 15, 8, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 32, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515275 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515275 Building ZINC001721515371 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515371 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/559 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCNC(N)=O)CCCC1) `ZINC001721515371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721515371 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCNC(N)=O)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 6, 8, 16, 16, 16, 41, 48, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 16, 41, 41, 48, 48, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/560 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCNC(N)=O)CCCC1) `ZINC001721515371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721515371 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCNC(N)=O)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 7, 16, 16, 16, 43, 46, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 16, 43, 43, 46, 46, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515371 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 Building ZINC001721515371 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515371 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 559) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCNC(N)=O)CCCC1) `ZINC001721515371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721515371 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCNC(N)=O)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 6, 8, 16, 16, 16, 41, 48, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 16, 41, 41, 48, 48, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 560) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCNC(N)=O)CCCC1) `ZINC001721515371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721515371 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCNC(N)=O)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 7, 16, 16, 16, 43, 46, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 16, 43, 43, 46, 46, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515371 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515371 Building ZINC001721515391 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515391 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/561 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515391 none CC(=O)N[C@H](C)C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 15, 9, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 33, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/562 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515391 none CC(=O)N[C@H](C)C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 50, 32, 32, 19, 12, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 32, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515391 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 Building ZINC001721515391 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515391 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 561) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515391 none CC(=O)N[C@H](C)C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 15, 9, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 33, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 562) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C)C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515391 none CC(=O)N[C@H](C)C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 50, 32, 32, 19, 12, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 32, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515391 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515391 Building ZINC001721515392 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515392 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/563 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515392 none CC(=O)N[C@@H](C)C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 17, 11, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 33, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/564 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515392 none CC(=O)N[C@@H](C)C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 50, 34, 34, 14, 8, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 34, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515392 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 Building ZINC001721515392 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515392 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 563) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515392 none CC(=O)N[C@@H](C)C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 50, 33, 33, 17, 11, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 33, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 564) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721515392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721515392 none CC(=O)N[C@@H](C)C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 50, 34, 34, 14, 8, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 34, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515392 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515392 Building ZINC001721515717 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515717 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/565 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCC(=O)N2)CCCC1) `ZINC001721515717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721515717 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCC(=O)N2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 12, 26, 26, 33, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 26, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/566 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCC(=O)N2)CCCC1) `ZINC001721515717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721515717 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCC(=O)N2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 11, 27, 27, 37, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 27, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515717 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 Building ZINC001721515717 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721515717 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 565) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCC(=O)N2)CCCC1) `ZINC001721515717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721515717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721515717 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCC(=O)N2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 12, 26, 26, 33, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 26, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 566) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCC(=O)N2)CCCC1) `ZINC001721515717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721515717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721515717 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCC(=O)N2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 11, 27, 27, 37, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 27, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721515717 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721515717 Building ZINC001721522894 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721522894 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/567 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721522894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721522894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721522894 none C[C@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 24, 46, 46, 50, 50, 50, 24, 24, 24, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 46, 46, 46, 50, 50, 50, 50, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/568 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721522894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721522894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721522894 none C[C@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 31, 48, 48, 50, 50, 50, 31, 31, 31, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 48, 48, 48, 50, 50, 50, 50, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721522894 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 Building ZINC001721522894 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721522894 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 567) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721522894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721522894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721522894 none C[C@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 24, 46, 46, 50, 50, 50, 24, 24, 24, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 46, 46, 46, 50, 50, 50, 50, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 568) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721522894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721522894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721522894 none C[C@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 31, 48, 48, 50, 50, 50, 31, 31, 31, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 48, 48, 48, 50, 50, 50, 50, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721522894 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522894 Building ZINC001721522895 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721522895 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/569 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721522895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721522895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721522895 none C[C@@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 30, 47, 47, 50, 50, 50, 30, 30, 30, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 47, 47, 47, 50, 50, 50, 50, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/570 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721522895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721522895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721522895 none C[C@@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 31, 47, 47, 50, 50, 50, 31, 31, 31, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 47, 47, 47, 50, 50, 50, 50, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721522895 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 Building ZINC001721522895 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721522895 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 569) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721522895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721522895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721522895 none C[C@@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 30, 47, 47, 50, 50, 50, 30, 30, 30, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 47, 47, 47, 50, 50, 50, 50, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 570) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001721522895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721522895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721522895 none C[C@@H](CC(N)=O)C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 31, 47, 47, 50, 50, 50, 31, 31, 31, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 47, 47, 47, 50, 50, 50, 50, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721522895 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721522895 Building ZINC001721531103 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531103 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/571 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531103 none COC[C@@H](OC)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 31, 15, 31, 31, 38, 15, 15, 5, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 50, 50, 50, 45, 45, 38, 38, 38, 15, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/572 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531103 none COC[C@@H](OC)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 38, 20, 38, 38, 46, 20, 20, 10, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 50, 50, 50, 48, 48, 46, 46, 46, 20, 10, 10, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531103 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 Building ZINC001721531103 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531103 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 571) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531103 none COC[C@@H](OC)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 31, 15, 31, 31, 38, 15, 15, 5, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 50, 50, 50, 45, 45, 38, 38, 38, 15, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 572) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531103 none COC[C@@H](OC)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 38, 20, 38, 38, 46, 20, 20, 10, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 50, 50, 50, 48, 48, 46, 46, 46, 20, 10, 10, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531103 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531103 Building ZINC001721531104 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531104 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/573 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531104 none COC[C@H](OC)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 33, 14, 33, 33, 39, 14, 14, 5, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 50, 50, 50, 47, 47, 39, 39, 39, 14, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/574 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531104 none COC[C@H](OC)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 17, 39, 39, 39, 17, 17, 9, 4, 3, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 6, 6, 50, 50, 50, 50, 50, 39, 39, 39, 17, 9, 9, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 233 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531104 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 Building ZINC001721531104 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531104 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 573) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531104 none COC[C@H](OC)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 33, 14, 33, 33, 39, 14, 14, 5, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 50, 50, 50, 47, 47, 39, 39, 39, 14, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 574) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531104 none COC[C@H](OC)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 17, 39, 39, 39, 17, 17, 9, 4, 3, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 6, 6, 50, 50, 50, 50, 50, 39, 39, 39, 17, 9, 9, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 233 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531104 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531104 Building ZINC001721531105 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531105 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/575 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531105 none COC[C@@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 46, 37, 23, 37, 37, 38, 23, 23, 14, 6, 3, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 8, 8, 48, 48, 48, 46, 46, 38, 38, 38, 23, 14, 14, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/576 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531105 none COC[C@@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 33, 13, 33, 33, 37, 13, 13, 5, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 50, 50, 50, 48, 48, 37, 37, 37, 13, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 227 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531105 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 Building ZINC001721531105 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531105 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 575) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531105 none COC[C@@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 46, 37, 23, 37, 37, 38, 23, 23, 14, 6, 3, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 8, 8, 48, 48, 48, 46, 46, 38, 38, 38, 23, 14, 14, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 576) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531105 none COC[C@@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 33, 13, 33, 33, 37, 13, 13, 5, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 50, 50, 50, 48, 48, 37, 37, 37, 13, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 227 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531105 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531105 Building ZINC001721531106 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531106 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/577 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531106 none COC[C@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 40, 19, 40, 40, 46, 19, 19, 9, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 5, 5, 50, 50, 50, 48, 48, 46, 46, 46, 19, 9, 9, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 232 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/578 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531106 none COC[C@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 31, 14, 31, 31, 40, 14, 14, 7, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 49, 49, 49, 45, 45, 40, 40, 40, 14, 7, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531106 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 Building ZINC001721531106 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531106 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 577) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531106 none COC[C@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 40, 19, 40, 40, 46, 19, 19, 9, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 5, 5, 50, 50, 50, 48, 48, 46, 46, 46, 19, 9, 9, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 232 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 578) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721531106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721531106 none COC[C@H](OC)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 31, 14, 31, 31, 40, 14, 14, 7, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 49, 49, 49, 45, 45, 40, 40, 40, 14, 7, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531106 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531106 Building ZINC001721531611 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531611 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/579 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721531611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721531611 none CCn1cc(C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 24, 24, 24, 10, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 9, 9, 31, 31, 50, 50, 50, 50, 50, 31, 24, 10, 10, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/580 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721531611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721531611 none CCn1cc(C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 28, 28, 23, 23, 23, 14, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 10, 10, 28, 28, 49, 49, 49, 49, 49, 28, 23, 14, 14, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 240 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531611 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 Building ZINC001721531611 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531611 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 579) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721531611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721531611 none CCn1cc(C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 24, 24, 24, 10, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 9, 9, 31, 31, 50, 50, 50, 50, 50, 31, 24, 10, 10, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 580) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721531611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721531611 none CCn1cc(C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 28, 28, 23, 23, 23, 14, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 10, 10, 28, 28, 49, 49, 49, 49, 49, 28, 23, 14, 14, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 240 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531611 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531611 Building ZINC001721531612 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531612 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/581 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721531612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721531612 none CCn1cc(C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 28, 28, 28, 22, 22, 22, 13, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 28, 28, 46, 46, 46, 46, 46, 28, 22, 13, 13, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/582 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721531612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721531612 none CCn1cc(C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 29, 29, 29, 23, 23, 23, 11, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 9, 9, 29, 29, 48, 48, 48, 48, 48, 29, 23, 11, 11, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531612 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 Building ZINC001721531612 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721531612 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 581) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721531612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721531612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721531612 none CCn1cc(C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 28, 28, 28, 22, 22, 22, 13, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 28, 28, 46, 46, 46, 46, 46, 28, 22, 13, 13, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 582) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001721531612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721531612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721531612 none CCn1cc(C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 29, 29, 29, 23, 23, 23, 11, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 9, 9, 29, 29, 48, 48, 48, 48, 48, 29, 23, 11, 11, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721531612 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721531612 Building ZINC001721532159 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721532159 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/583 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721532159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532159 none C[C@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 18, 36, 36, 47, 50, 50, 18, 18, 10, 5, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 7, 7, 36, 36, 36, 47, 47, 50, 50, 18, 10, 10, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 228 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/584 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721532159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532159 none C[C@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 10, 30, 30, 47, 50, 50, 10, 10, 4, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 30, 30, 30, 47, 47, 50, 50, 10, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721532159 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 Building ZINC001721532159 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721532159 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 583) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721532159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532159 none C[C@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 18, 36, 36, 47, 50, 50, 18, 18, 10, 5, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 7, 7, 36, 36, 36, 47, 47, 50, 50, 18, 10, 10, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 228 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 584) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721532159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532159 none C[C@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 10, 30, 30, 47, 50, 50, 10, 10, 4, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 30, 30, 30, 47, 47, 50, 50, 10, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721532159 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532159 Building ZINC001721532160 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721532160 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/585 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721532160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532160 none C[C@@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 12, 34, 34, 49, 50, 50, 12, 12, 4, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 34, 34, 34, 49, 49, 50, 50, 12, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/586 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721532160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532160 none C[C@@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 16, 38, 38, 47, 50, 50, 16, 16, 8, 5, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 38, 38, 38, 47, 47, 50, 50, 16, 8, 8, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721532160 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 Building ZINC001721532160 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721532160 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 585) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721532160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532160 none C[C@@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 12, 34, 34, 49, 50, 50, 12, 12, 4, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 34, 34, 34, 49, 49, 50, 50, 12, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 586) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721532160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532160 none C[C@@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 16, 38, 38, 47, 50, 50, 16, 16, 8, 5, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 38, 38, 38, 47, 47, 50, 50, 16, 8, 8, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721532160 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532160 Building ZINC001721532161 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721532161 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/587 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721532161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532161 none C[C@@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 34, 34, 48, 50, 50, 18, 18, 9, 5, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 34, 34, 34, 48, 48, 50, 50, 18, 9, 9, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/588 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721532161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532161 none C[C@@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 10, 29, 29, 46, 50, 50, 10, 10, 4, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 29, 29, 29, 46, 46, 50, 50, 10, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721532161 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 Building ZINC001721532161 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721532161 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 587) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721532161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532161 none C[C@@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 34, 34, 48, 50, 50, 18, 18, 9, 5, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 34, 34, 34, 48, 48, 50, 50, 18, 9, 9, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 588) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721532161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532161 none C[C@@H](CC(N)=O)C(=O)NC[C@@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 10, 29, 29, 46, 50, 50, 10, 10, 4, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 29, 29, 29, 46, 46, 50, 50, 10, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721532161 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532161 Building ZINC001721532162 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721532162 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/589 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721532162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532162 none C[C@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 12, 34, 34, 46, 50, 50, 12, 12, 5, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 34, 34, 34, 46, 46, 50, 50, 12, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/590 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721532162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532162 none C[C@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 34, 34, 48, 50, 50, 18, 18, 9, 5, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 34, 34, 34, 48, 48, 50, 50, 18, 9, 9, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721532162 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 Building ZINC001721532162 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721532162 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 589) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721532162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532162 none C[C@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 12, 34, 34, 46, 50, 50, 12, 12, 5, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 34, 34, 34, 46, 46, 50, 50, 12, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 590) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721532162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721532162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721532162 none C[C@H](CC(N)=O)C(=O)NC[C@](C)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 34, 34, 48, 50, 50, 18, 18, 9, 5, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 34, 34, 34, 48, 48, 50, 50, 18, 9, 9, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721532162 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721532162 Building ZINC001721534797 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721534797 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/591 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721534797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534797 none C[C@@H](C(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 21, 41, 21, 21, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 26, 26, 41, 49, 49, 49, 49, 41, 41, 41, 21, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 49, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/592 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721534797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534797 none C[C@@H](C(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 16, 37, 16, 16, 16, 8, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 22, 22, 37, 47, 47, 47, 47, 37, 37, 37, 16, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 47, 47] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721534797 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 Building ZINC001721534797 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721534797 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 591) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721534797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534797 none C[C@@H](C(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 21, 41, 21, 21, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 26, 26, 41, 49, 49, 49, 49, 41, 41, 41, 21, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 49, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 592) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721534797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534797 none C[C@@H](C(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 16, 37, 16, 16, 16, 8, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 22, 22, 37, 47, 47, 47, 47, 37, 37, 37, 16, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 47, 47] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721534797 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534797 Building ZINC001721534798 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721534798 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/593 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721534798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534798 none C[C@H](C(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 17, 39, 17, 17, 17, 8, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 20, 20, 39, 49, 49, 49, 49, 39, 39, 39, 17, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 49, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/594 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721534798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534798 none C[C@H](C(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 21, 41, 21, 21, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 26, 26, 41, 49, 49, 49, 49, 41, 41, 41, 21, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 49, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721534798 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 Building ZINC001721534798 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721534798 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 593) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721534798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534798 none C[C@H](C(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 17, 39, 17, 17, 17, 8, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 20, 20, 39, 49, 49, 49, 49, 39, 39, 39, 17, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 49, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 594) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721534798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534798 none C[C@H](C(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 21, 41, 21, 21, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 26, 26, 41, 49, 49, 49, 49, 41, 41, 41, 21, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 49, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721534798 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534798 Building ZINC001721534799 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721534799 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/595 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721534799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534799 none C[C@@H](C(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 17, 44, 17, 17, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 18, 18, 44, 50, 50, 50, 50, 44, 44, 44, 17, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/596 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/596' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721534799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534799 none C[C@@H](C(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 23, 46, 23, 23, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 46, 50, 50, 50, 50, 46, 46, 46, 23, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721534799 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 Building ZINC001721534799 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721534799 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 595) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721534799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534799 none C[C@@H](C(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 17, 44, 17, 17, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 18, 18, 44, 50, 50, 50, 50, 44, 44, 44, 17, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 596) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721534799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534799 none C[C@@H](C(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 23, 46, 23, 23, 20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 46, 50, 50, 50, 50, 46, 46, 46, 23, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721534799 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534799 Building ZINC001721534800 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721534800 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/597 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721534800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534800 none C[C@H](C(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 29, 47, 29, 29, 24, 10, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 47, 50, 50, 50, 50, 47, 47, 47, 29, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/598 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/598' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721534800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534800 none C[C@H](C(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 20, 43, 20, 20, 18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 24, 24, 43, 48, 48, 48, 48, 43, 43, 43, 20, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 48, 48] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721534800 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 Building ZINC001721534800 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721534800 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 597) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721534800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534800 none C[C@H](C(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 29, 47, 29, 29, 24, 10, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 47, 50, 50, 50, 50, 47, 47, 47, 29, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 598) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001721534800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721534800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721534800 none C[C@H](C(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 20, 43, 20, 20, 18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 24, 24, 43, 48, 48, 48, 48, 43, 43, 43, 20, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 48, 48] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721534800 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721534800 Building ZINC001721540071 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721540071 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/599 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)CCCC(N)=O)C1CC1) `ZINC001721540071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721540071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721540071 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 2, 2, 2, 8, 17, 17, 19, 19, 19, 36, 34, 46, 46, 46, 17, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 17, 17, 17, 19, 36, 36, 39, 39, 43, 45, 46, 46, 26, 26, 26, 26, 26] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 273 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/600 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/600' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)CCCC(N)=O)C1CC1) `ZINC001721540071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721540071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721540071 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 10, 22, 22, 26, 26, 26, 38, 33, 46, 47, 47, 22, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 22, 22, 22, 26, 38, 38, 39, 39, 44, 42, 47, 47, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 288 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721540071 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 Building ZINC001721540071 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721540071 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 599) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)CCCC(N)=O)C1CC1) `ZINC001721540071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721540071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721540071 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 2, 2, 2, 8, 17, 17, 19, 19, 19, 36, 34, 46, 46, 46, 17, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 17, 17, 17, 19, 36, 36, 39, 39, 43, 45, 46, 46, 26, 26, 26, 26, 26] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 273 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 600) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)CCCC(N)=O)C1CC1) `ZINC001721540071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721540071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721540071 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 10, 22, 22, 26, 26, 26, 38, 33, 46, 47, 47, 22, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 22, 22, 22, 26, 38, 38, 39, 39, 44, 42, 47, 47, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 288 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721540071 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540071 Building ZINC001721540072 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721540072 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/601 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)CCCC(N)=O)C1CC1) `ZINC001721540072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721540072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721540072 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 21, 21, 23, 23, 23, 36, 33, 46, 46, 46, 21, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 21, 23, 36, 36, 38, 38, 43, 44, 46, 46, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 279 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/602 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)CCCC(N)=O)C1CC1) `ZINC001721540072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721540072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721540072 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 14, 16, 16, 16, 34, 30, 44, 45, 45, 14, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 14, 14, 14, 16, 34, 34, 37, 37, 42, 40, 45, 45, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 271 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721540072 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 Building ZINC001721540072 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721540072 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 601) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)CCCC(N)=O)C1CC1) `ZINC001721540072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721540072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721540072 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 21, 21, 23, 23, 23, 36, 33, 46, 46, 46, 21, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 21, 23, 36, 36, 38, 38, 43, 44, 46, 46, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 279 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 602) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)CCCC(N)=O)C1CC1) `ZINC001721540072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721540072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721540072 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 14, 16, 16, 16, 34, 30, 44, 45, 45, 14, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 14, 14, 14, 16, 34, 34, 37, 37, 42, 40, 45, 45, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 271 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721540072 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721540072 Building ZINC001721541171 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721541171 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/603 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721541171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721541171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721541171 none Cn1cncc1CC(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 42, 23, 23, 23, 20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 46, 46, 46, 46, 46, 42, 42, 23, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/604 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721541171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721541171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721541171 none Cn1cncc1CC(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 37, 14, 14, 14, 14, 6, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 21, 21, 43, 43, 43, 43, 43, 37, 37, 14, 14, 14, 14, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721541171 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 Building ZINC001721541171 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721541171 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 603) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721541171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721541171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721541171 none Cn1cncc1CC(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 42, 23, 23, 23, 20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 46, 46, 46, 46, 46, 42, 42, 23, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 604) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721541171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721541171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721541171 none Cn1cncc1CC(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 37, 14, 14, 14, 14, 6, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 21, 21, 43, 43, 43, 43, 43, 37, 37, 14, 14, 14, 14, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721541171 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541171 Building ZINC001721541172 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721541172 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/605 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721541172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721541172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721541172 none Cn1cncc1CC(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 43, 18, 18, 18, 18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 23, 48, 48, 48, 48, 48, 43, 43, 18, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/606 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721541172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721541172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721541172 none Cn1cncc1CC(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 42, 23, 23, 23, 20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 46, 46, 46, 46, 46, 42, 42, 23, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721541172 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 Building ZINC001721541172 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721541172 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 605) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721541172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721541172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721541172 none Cn1cncc1CC(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 43, 18, 18, 18, 18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 23, 48, 48, 48, 48, 48, 43, 43, 18, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 606) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721541172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721541172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721541172 none Cn1cncc1CC(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 42, 23, 23, 23, 20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 46, 46, 46, 46, 46, 42, 42, 23, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721541172 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721541172 Building ZINC001721543203 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721543203 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/607 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721543203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721543203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721543203 none CN(C)CCC(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 47, 45, 19, 19, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 23, 23, 47, 47, 47, 47, 47, 47, 45, 45, 45, 45, 19, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/608 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721543203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721543203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721543203 none CN(C)CCC(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 23, 23, 23, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 23, 21, 21, 21, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721543203 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 Building ZINC001721543203 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721543203 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 607) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721543203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721543203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721543203 none CN(C)CCC(=O)N[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 47, 45, 19, 19, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 23, 23, 47, 47, 47, 47, 47, 47, 45, 45, 45, 45, 19, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 608) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721543203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721543203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721543203 none CN(C)CCC(=O)N[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 23, 23, 23, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 23, 21, 21, 21, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721543203 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543203 Building ZINC001721543204 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721543204 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/609 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721543204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721543204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721543204 none CN(C)CCC(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 22, 22, 22, 20, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 22, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/610 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721543204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721543204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721543204 none CN(C)CCC(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 37, 36, 13, 13, 13, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 19, 19, 37, 37, 37, 37, 37, 37, 36, 36, 36, 36, 13, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721543204 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 Building ZINC001721543204 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721543204 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 609) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721543204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721543204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721543204 none CN(C)CCC(=O)N[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 22, 22, 22, 20, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 22, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 610) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001721543204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721543204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721543204 none CN(C)CCC(=O)N[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 37, 36, 13, 13, 13, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 19, 19, 37, 37, 37, 37, 37, 37, 36, 36, 36, 36, 13, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721543204 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721543204 Building ZINC001721546115 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546115 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/611 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)Cn1cncn1)C1CC1) `ZINC001721546115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721546115 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)Cn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 14, 14, 14, 14, 39, 47, 47, 47, 47, 14, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 14, 14, 14, 14, 39, 39, 47, 47, 16, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/612 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)Cn1cncn1)C1CC1) `ZINC001721546115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721546115 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)Cn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 17, 17, 17, 44, 50, 50, 50, 50, 15, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 17, 44, 44, 50, 50, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546115 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 Building ZINC001721546115 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546115 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 611) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)Cn1cncn1)C1CC1) `ZINC001721546115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721546115 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)Cn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 14, 14, 14, 14, 39, 47, 47, 47, 47, 14, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 14, 14, 14, 14, 39, 39, 47, 47, 16, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 612) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)Cn1cncn1)C1CC1) `ZINC001721546115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721546115 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@](C)(NC(=O)Cn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 17, 17, 17, 44, 50, 50, 50, 50, 15, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 17, 44, 44, 50, 50, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546115 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546115 Building ZINC001721546116 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546116 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/613 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)Cn1cncn1)C1CC1) `ZINC001721546116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721546116 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)Cn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 17, 17, 17, 41, 48, 48, 48, 48, 15, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 15, 17, 41, 41, 48, 48, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/614 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)Cn1cncn1)C1CC1) `ZINC001721546116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721546116 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)Cn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 12, 12, 29, 40, 40, 40, 40, 12, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 12, 12, 29, 29, 40, 40, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546116 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 Building ZINC001721546116 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546116 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 613) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)Cn1cncn1)C1CC1) `ZINC001721546116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721546116 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)Cn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 17, 17, 17, 41, 48, 48, 48, 48, 15, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 15, 17, 41, 41, 48, 48, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 614) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)Cn1cncn1)C1CC1) `ZINC001721546116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721546116 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@](C)(NC(=O)Cn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 12, 12, 29, 40, 40, 40, 40, 12, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 12, 12, 29, 29, 40, 40, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546116 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546116 Building ZINC001721546397 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546397 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/615 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546397 none C[C@H]1CCCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 49, 50, 50, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 49, 49, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/616 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546397 none C[C@H]1CCCC[C@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 49, 50, 50, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 49, 49, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546397 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 Building ZINC001721546397 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546397 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 615) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546397 none C[C@H]1CCCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 49, 50, 50, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 49, 49, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 616) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546397 none C[C@H]1CCCC[C@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 49, 50, 50, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 49, 49, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546397 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546397 Building ZINC001721546398 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546398 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/617 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546398 none C[C@@H]1CCCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 48, 50, 50, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 48, 48, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/618 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546398 none C[C@@H]1CCCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 48, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 48, 48, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546398 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 Building ZINC001721546398 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546398 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 617) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546398 none C[C@@H]1CCCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 48, 50, 50, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 48, 48, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 618) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546398 none C[C@@H]1CCCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 48, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 48, 48, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546398 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546398 Building ZINC001721546399 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546399 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/619 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546399 none C[C@H]1CCCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 50, 50, 50, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/620 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/620' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546399 none C[C@H]1CCCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546399 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 Building ZINC001721546399 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546399 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 619) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546399 none C[C@H]1CCCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 50, 50, 50, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 620) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546399 none C[C@H]1CCCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546399 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546399 Building ZINC001721546400 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546400 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/621 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546400 none C[C@@H]1CCCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 48, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 48, 48, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/622 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546400 none C[C@@H]1CCCC[C@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 49, 50, 50, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 49, 49, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546400 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 Building ZINC001721546400 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721546400 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 621) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721546400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546400 none C[C@@H]1CCCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 48, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 48, 48, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 622) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O) `ZINC001721546400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721546400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721546400 none C[C@@H]1CCCC[C@]1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 49, 50, 50, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 49, 49, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721546400 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721546400 Building ZINC001721556032 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721556032 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/623 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001721556032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721556032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721556032 none Cn1ncc(C(=O)N2CCC(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 27, 49, 27, 27, 27, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/624 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001721556032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721556032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721556032 none Cn1ncc(C(=O)N2CCC(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 28, 28, 28, 17, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721556032 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 Building ZINC001721556032 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721556032 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 623) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001721556032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721556032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721556032 none Cn1ncc(C(=O)N2CCC(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 27, 49, 27, 27, 27, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 624) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001721556032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721556032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721556032 none Cn1ncc(C(=O)N2CCC(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 50, 28, 28, 28, 17, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721556032 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721556032 Building ZINC001721561562 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721561562 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/625 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)c2nccnc2N)CC1) `ZINC001721561562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721561562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721561562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)c2nccnc2N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 17, 17, 17, 17, 17, 17, 34, 34, 34, 50, 50, 50, 50, 50, 50, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 34, 50, 50, 50, 50, 17, 17, 17, 17] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/626 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)c2nccnc2N)CC1) `ZINC001721561562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721561562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721561562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)c2nccnc2N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 16, 16, 16, 16, 16, 16, 35, 35, 35, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 16, 16, 35, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721561562 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 Building ZINC001721561562 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721561562 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 625) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)c2nccnc2N)CC1) `ZINC001721561562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721561562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721561562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)c2nccnc2N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 17, 17, 17, 17, 17, 17, 34, 34, 34, 50, 50, 50, 50, 50, 50, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 34, 50, 50, 50, 50, 17, 17, 17, 17] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 626) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)c2nccnc2N)CC1) `ZINC001721561562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721561562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721561562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)c2nccnc2N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 16, 16, 16, 16, 16, 16, 35, 35, 35, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 16, 16, 35, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721561562 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721561562 Building ZINC001721567215 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721567215 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/627 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CCn1cccn1) `ZINC001721567215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721567215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721567215 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 25, 28, 28, 41, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 25, 25, 25, 25, 25, 25, 41, 41, 42, 42, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/628 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CCn1cccn1) `ZINC001721567215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721567215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721567215 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 20, 20, 37, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 17, 17, 17, 17, 17, 17, 37, 37, 39, 39, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721567215 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 Building ZINC001721567215 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721567215 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 627) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CCn1cccn1) `ZINC001721567215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721567215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721567215 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 25, 28, 28, 41, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 25, 25, 25, 25, 25, 25, 41, 41, 42, 42, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 628) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CCn1cccn1) `ZINC001721567215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721567215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721567215 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)CCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 20, 20, 37, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 17, 17, 17, 17, 17, 17, 37, 37, 39, 39, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721567215 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567215 Building ZINC001721567697 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721567697 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/629 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@@H]1COCCO1) `ZINC001721567697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721567697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721567697 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@@H]1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 29, 29, 29, 29, 29, 29, 37, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/630 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@@H]1COCCO1) `ZINC001721567697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721567697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721567697 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@@H]1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 26, 26, 26, 26, 26, 26, 35, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721567697 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 Building ZINC001721567697 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721567697 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 629) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@@H]1COCCO1) `ZINC001721567697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721567697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721567697 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@@H]1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 29, 29, 29, 29, 29, 29, 37, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 630) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@@H]1COCCO1) `ZINC001721567697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721567697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721567697 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@@H]1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 26, 26, 26, 26, 26, 26, 35, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721567697 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567697 Building ZINC001721567698 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721567698 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/631 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1COCCO1) `ZINC001721567698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721567698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721567698 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 27, 27, 27, 27, 27, 27, 36, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/632 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1COCCO1) `ZINC001721567698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721567698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721567698 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 29, 29, 29, 29, 29, 29, 36, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721567698 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 Building ZINC001721567698 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721567698 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 631) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1COCCO1) `ZINC001721567698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721567698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721567698 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 27, 27, 27, 27, 27, 27, 36, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 632) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1COCCO1) `ZINC001721567698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721567698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721567698 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 29, 29, 29, 29, 29, 29, 36, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721567698 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721567698 Building ZINC001721569655 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721569655 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/633 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)Cn1ccccc1=O) `ZINC001721569655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721569655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721569655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 29, 29, 29, 29, 29, 29, 35, 35, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/634 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)Cn1ccccc1=O) `ZINC001721569655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721569655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721569655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 25, 25, 25, 25, 25, 25, 31, 31, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 25, 25, 25, 25, 25, 25, 48, 48, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721569655 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 Building ZINC001721569655 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721569655 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 633) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)Cn1ccccc1=O) `ZINC001721569655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721569655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721569655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 29, 29, 29, 29, 29, 29, 35, 35, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 634) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)Cn1ccccc1=O) `ZINC001721569655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721569655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721569655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 25, 25, 25, 25, 25, 25, 31, 31, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 25, 25, 25, 25, 25, 25, 48, 48, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721569655 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721569655 Building ZINC001721586422 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586422 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/635 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586422 none C[C@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 12, 15, 15, 15, 26, 26, 26, 26, 50, 50, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 15, 26, 50, 50, 50, 50, 26, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/636 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586422 none C[C@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 10, 14, 18, 18, 18, 25, 25, 25, 25, 50, 50, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 14, 18, 25, 50, 50, 50, 50, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586422 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 Building ZINC001721586422 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586422 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 635) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586422 none C[C@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 12, 15, 15, 15, 26, 26, 26, 26, 50, 50, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 15, 26, 50, 50, 50, 50, 26, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 636) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586422 none C[C@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 10, 14, 18, 18, 18, 25, 25, 25, 25, 50, 50, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 14, 18, 25, 50, 50, 50, 50, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586422 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586422 Building ZINC001721586423 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586423 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/637 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586423 none C[C@@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 10, 15, 19, 19, 19, 25, 25, 25, 25, 50, 50, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 15, 15, 19, 25, 50, 50, 50, 50, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/638 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586423 none C[C@@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 12, 16, 16, 16, 26, 26, 26, 26, 50, 50, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 16, 26, 50, 50, 50, 50, 26, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586423 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 Building ZINC001721586423 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586423 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 637) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586423 none C[C@@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 10, 15, 19, 19, 19, 25, 25, 25, 25, 50, 50, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 15, 15, 19, 25, 50, 50, 50, 50, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 638) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586423 none C[C@@H](CNC(=O)c1cnn(CCF)c1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 12, 16, 16, 16, 26, 26, 26, 26, 50, 50, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 16, 26, 50, 50, 50, 50, 26, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586423 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586423 Building ZINC001721586516 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586516 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/639 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586516 none C[C@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 12, 16, 20, 20, 20, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 20, 45, 45, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/640 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586516 none C[C@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 11, 16, 16, 16, 16, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 16, 16, 45, 45, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586516 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 Building ZINC001721586516 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586516 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 639) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586516 none C[C@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 12, 16, 20, 20, 20, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 20, 45, 45, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 640) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586516 none C[C@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 11, 16, 16, 16, 16, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 16, 16, 45, 45, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586516 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586516 Building ZINC001721586517 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586517 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/641 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586517 none C[C@@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 12, 16, 20, 20, 20, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 20, 45, 45, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/642 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/642' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586517 none C[C@@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 12, 15, 18, 18, 18, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 18, 45, 45, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586517 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 Building ZINC001721586517 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586517 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 641) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586517 none C[C@@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 12, 16, 20, 20, 20, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 20, 45, 45, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 642) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586517 none C[C@@H](CNC(=O)[C@@H]1C[C@H]1c1cnc[nH]1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 12, 15, 18, 18, 18, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 18, 45, 45, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586517 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586517 Building ZINC001721586666 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586666 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/643 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721586666 none C[C@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 12, 16, 20, 20, 20, 43, 49, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 20, 43, 43, 49, 49, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/644 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/644' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721586666 none C[C@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 13, 18, 23, 23, 23, 46, 48, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 23, 46, 46, 48, 48, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586666 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 Building ZINC001721586666 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586666 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 643) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721586666 none C[C@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 12, 16, 20, 20, 20, 43, 49, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 20, 43, 43, 49, 49, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 644) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721586666 none C[C@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 13, 18, 23, 23, 23, 46, 48, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 23, 46, 46, 48, 48, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586666 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586666 Building ZINC001721586667 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586667 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/645 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721586667 none C[C@@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 13, 18, 23, 23, 23, 46, 48, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 23, 46, 46, 48, 48, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/646 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721586667 none C[C@@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 12, 16, 20, 20, 20, 43, 49, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 20, 43, 43, 49, 49, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586667 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 Building ZINC001721586667 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586667 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 645) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721586667 none C[C@@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 13, 18, 23, 23, 23, 46, 48, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 23, 46, 46, 48, 48, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 646) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721586667 none C[C@@H](CNC(=O)CCc1nccn1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 12, 16, 20, 20, 20, 43, 49, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 20, 43, 43, 49, 49, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586667 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586667 Building ZINC001721586668 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586668 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/647 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586668 none C[C@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 26, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 26, 26, 37, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/648 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/648' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586668 none C[C@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 15, 26, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 39, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586668 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 Building ZINC001721586668 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586668 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 647) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586668 none C[C@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 26, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 26, 26, 37, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 648) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586668 none C[C@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 15, 26, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 39, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586668 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586668 Building ZINC001721586669 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586669 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/649 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586669 none C[C@@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 15, 26, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 39, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/650 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586669 none C[C@@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 15, 25, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 25, 25, 36, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586669 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 Building ZINC001721586669 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586669 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 649) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586669 none C[C@@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 15, 26, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 39, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 650) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586669 none C[C@@H](CNC(=O)c1cccc(=O)n1C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 15, 25, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 25, 25, 36, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586669 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586669 Building ZINC001721586728 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586728 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/651 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586728 none C[C@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 17, 25, 30, 30, 30, 39, 39, 30, 30, 50, 50, 39, 39, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 17, 17, 17, 25, 25, 30, 39, 39, 50, 50, 39, 39, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/652 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586728 none C[C@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 19, 19, 28, 31, 31, 31, 37, 37, 31, 31, 50, 50, 37, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 28, 28, 31, 37, 37, 50, 50, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586728 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 Building ZINC001721586728 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586728 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 651) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586728 none C[C@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 17, 25, 30, 30, 30, 39, 39, 30, 30, 50, 50, 39, 39, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 17, 17, 17, 25, 25, 30, 39, 39, 50, 50, 39, 39, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 652) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586728 none C[C@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 19, 19, 28, 31, 31, 31, 37, 37, 31, 31, 50, 50, 37, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 28, 28, 31, 37, 37, 50, 50, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586728 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586728 Building ZINC001721586729 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586729 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/653 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586729 none C[C@@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 17, 26, 29, 29, 29, 36, 36, 29, 29, 50, 50, 36, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 26, 26, 29, 36, 36, 50, 50, 36, 36, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/654 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586729 none C[C@@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 16, 24, 29, 29, 29, 37, 37, 29, 37, 50, 50, 37, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 24, 24, 29, 37, 37, 50, 50, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 231 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586729 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 Building ZINC001721586729 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586729 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 653) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586729 none C[C@@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 17, 26, 29, 29, 29, 36, 36, 29, 29, 50, 50, 36, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 26, 26, 29, 36, 36, 50, 50, 36, 36, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 654) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721586729 none C[C@@H](CNC(=O)c1ccc(C(N)=O)cc1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 16, 24, 29, 29, 29, 37, 37, 29, 37, 50, 50, 37, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 24, 24, 29, 37, 37, 50, 50, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 231 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586729 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586729 Building ZINC001721586732 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586732 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/655 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586732 none Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 22, 10, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 40, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/656 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586732 none Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 20, 8, 20, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 38, 38, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586732 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 Building ZINC001721586732 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586732 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 655) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586732 none Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 22, 10, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 40, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 656) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586732 none Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 20, 8, 20, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 38, 38, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586732 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586732 Building ZINC001721586733 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586733 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/657 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)NC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586733 none Cc1nn(C)c(F)c1C(=O)NC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 20, 8, 20, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 38, 38, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/658 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)NC[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586733 none Cc1nn(C)c(F)c1C(=O)NC[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 22, 10, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 41, 41, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586733 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 Building ZINC001721586733 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721586733 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 657) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)NC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721586733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721586733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586733 none Cc1nn(C)c(F)c1C(=O)NC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 20, 8, 20, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 38, 38, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 658) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)NC[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721586733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721586733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721586733 none Cc1nn(C)c(F)c1C(=O)NC[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 22, 10, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 41, 41, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721586733 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721586733 Building ZINC001721587064 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587064 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/659 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587064 none C[C@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 12, 19, 19, 19, 43, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 19, 41, 41, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/660 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587064 none C[C@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 16, 23, 23, 23, 44, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 23, 42, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587064 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 Building ZINC001721587064 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587064 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 659) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587064 none C[C@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 12, 19, 19, 19, 43, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 19, 41, 41, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 660) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587064 none C[C@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 16, 23, 23, 23, 44, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 23, 42, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587064 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587064 Building ZINC001721587065 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587065 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/661 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587065 none C[C@@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 16, 23, 23, 23, 44, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 23, 42, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/662 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587065 none C[C@@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 12, 19, 19, 19, 43, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 19, 41, 41, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587065 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 Building ZINC001721587065 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587065 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 661) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587065 none C[C@@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 16, 23, 23, 23, 44, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 23, 42, 42, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 662) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587065 none C[C@@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 12, 19, 19, 19, 43, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 19, 41, 41, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587065 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587065 Building ZINC001721587066 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587066 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/663 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587066 none C[C@@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 14, 14, 18, 24, 24, 24, 47, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 18, 18, 24, 46, 46, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/664 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587066 none C[C@@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 15, 20, 20, 20, 46, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 20, 42, 42, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587066 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 Building ZINC001721587066 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587066 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 663) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587066 none C[C@@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 14, 14, 18, 24, 24, 24, 47, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 18, 18, 24, 46, 46, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 664) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587066 none C[C@@H](CNC(=O)C[C@@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 15, 20, 20, 20, 46, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 20, 42, 42, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587066 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587066 Building ZINC001721587067 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587067 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/665 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587067 none C[C@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 15, 20, 20, 20, 46, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 20, 42, 42, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/666 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587067 none C[C@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 14, 14, 17, 23, 23, 23, 47, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 17, 17, 23, 46, 46, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587067 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 Building ZINC001721587067 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587067 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 665) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587067 none C[C@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 15, 20, 20, 20, 46, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 20, 42, 42, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 666) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587067 none C[C@H](CNC(=O)C[C@H]1CCN(C)C1=O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 14, 14, 17, 23, 23, 23, 47, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 17, 17, 23, 46, 46, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587067 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587067 Building ZINC001721587076 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587076 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/667 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587076 none C[C@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 9, 12, 12, 12, 35, 43, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 12, 35, 35, 43, 43, 50, 50, 50, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/668 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/668' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587076 none C[C@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 12, 16, 16, 16, 37, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 12, 12, 16, 37, 37, 45, 45, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587076 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 Building ZINC001721587076 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587076 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 667) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587076 none C[C@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 9, 12, 12, 12, 35, 43, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 12, 35, 35, 43, 43, 50, 50, 50, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 668) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587076 none C[C@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 12, 16, 16, 16, 37, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 12, 12, 16, 37, 37, 45, 45, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587076 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587076 Building ZINC001721587077 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587077 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/669 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587077 none C[C@@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 13, 16, 16, 16, 38, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 16, 38, 38, 45, 45, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/670 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587077 none C[C@@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 9, 12, 12, 12, 34, 43, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 12, 34, 34, 43, 43, 50, 50, 50, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587077 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 Building ZINC001721587077 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587077 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 669) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587077 none C[C@@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 13, 16, 16, 16, 38, 45, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 16, 38, 38, 45, 45, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 670) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587077 none C[C@@H](CNC(=O)CCc1ccncn1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 9, 12, 12, 12, 34, 43, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 12, 34, 34, 43, 43, 50, 50, 50, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587077 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587077 Building ZINC001721587108 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587108 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/671 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587108 none C[C@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 12, 18, 27, 27, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/672 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/672' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587108 none C[C@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 17, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 17, 17, 26, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587108 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 Building ZINC001721587108 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587108 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 671) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587108 none C[C@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 12, 18, 27, 27, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 672) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587108 none C[C@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 17, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 17, 17, 26, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587108 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587108 Building ZINC001721587109 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587109 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/673 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587109 none C[C@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 16, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 24, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/674 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587109 none C[C@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 18, 29, 29, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 18, 18, 29, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587109 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 Building ZINC001721587109 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587109 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 673) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587109 none C[C@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 16, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 24, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 674) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587109 none C[C@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 18, 29, 29, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 18, 18, 29, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587109 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587109 Building ZINC001721587110 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587110 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/675 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587110 none C[C@@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 18, 29, 29, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 18, 18, 29, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/676 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587110 none C[C@@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 16, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 24, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587110 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 Building ZINC001721587110 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587110 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 675) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587110 none C[C@@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 18, 29, 29, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 18, 18, 29, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 676) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587110 none C[C@@H](CNC(=O)[C@@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 16, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 16, 16, 24, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587110 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587110 Building ZINC001721587111 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587111 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/677 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587111 none C[C@@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 11, 17, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 17, 17, 26, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/678 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587111 none C[C@@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 12, 18, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 26, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587111 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 Building ZINC001721587111 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587111 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 677) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587111 none C[C@@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 11, 17, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 17, 17, 26, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 678) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721587111 none C[C@@H](CNC(=O)[C@H]1CCc2cncn2C1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 12, 18, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 26, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587111 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587111 Building ZINC001721587498 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587498 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/679 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)NC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721587498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721587498 none CCn1ccc(CC(=O)NC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 21, 10, 10, 10, 8, 7, 4, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 32, 32, 21, 21, 10, 8, 8, 7, 7, 7, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/680 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)NC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721587498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721587498 none CCn1ccc(CC(=O)NC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 26, 13, 13, 13, 9, 6, 4, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 31, 26, 26, 13, 9, 9, 6, 6, 6, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 244 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587498 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 Building ZINC001721587498 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587498 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 679) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)NC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721587498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721587498 none CCn1ccc(CC(=O)NC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 21, 10, 10, 10, 8, 7, 4, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 32, 32, 21, 21, 10, 8, 8, 7, 7, 7, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 680) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)NC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721587498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721587498 none CCn1ccc(CC(=O)NC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 26, 13, 13, 13, 9, 6, 4, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 31, 26, 26, 13, 9, 9, 6, 6, 6, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 244 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587498 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587498 Building ZINC001721587499 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587499 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/681 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)NC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721587499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721587499 none CCn1ccc(CC(=O)NC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 27, 14, 14, 14, 9, 6, 4, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 32, 32, 27, 27, 14, 9, 9, 6, 6, 6, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 248 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/682 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)NC[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721587499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721587499 none CCn1ccc(CC(=O)NC[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 22, 10, 10, 10, 7, 6, 4, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 31, 22, 22, 10, 7, 7, 6, 6, 6, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 229 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587499 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 Building ZINC001721587499 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587499 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 681) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)NC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721587499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721587499 none CCn1ccc(CC(=O)NC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 27, 14, 14, 14, 9, 6, 4, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 32, 32, 27, 27, 14, 9, 9, 6, 6, 6, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 248 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 682) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)NC[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001721587499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721587499 none CCn1ccc(CC(=O)NC[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 22, 10, 10, 10, 7, 6, 4, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 31, 22, 22, 10, 7, 7, 6, 6, 6, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 229 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587499 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587499 Building ZINC001721587836 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587836 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/683 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587836 none C[C@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 11, 13, 13, 13, 44, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 13, 44, 44, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/684 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/684' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587836 none C[C@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 11, 14, 14, 14, 42, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 11, 11, 14, 42, 42, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587836 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 Building ZINC001721587836 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587836 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 683) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587836 none C[C@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 11, 13, 13, 13, 44, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 13, 44, 44, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 684) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587836 none C[C@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 11, 14, 14, 14, 42, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 11, 11, 14, 42, 42, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587836 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587836 Building ZINC001721587837 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587837 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/685 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587837 none C[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 11, 14, 14, 14, 47, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 14, 46, 46, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/686 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587837 none C[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 13, 16, 16, 16, 46, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 16, 44, 44, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587837 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 Building ZINC001721587837 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587837 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 685) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587837 none C[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 11, 14, 14, 14, 47, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 14, 46, 46, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 686) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587837 none C[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 13, 16, 16, 16, 46, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 16, 44, 44, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587837 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587837 Building ZINC001721587838 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587838 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/687 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587838 none C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 11, 14, 14, 14, 42, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 11, 11, 14, 42, 42, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/688 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587838 none C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 11, 13, 13, 13, 44, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 13, 44, 44, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587838 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 Building ZINC001721587838 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587838 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 687) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587838 none C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 11, 14, 14, 14, 42, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 11, 11, 14, 42, 42, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 688) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587838 none C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 11, 13, 13, 13, 44, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 13, 44, 44, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587838 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587838 Building ZINC001721587839 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587839 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/689 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587839 none C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 13, 16, 16, 16, 46, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 16, 44, 44, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/690 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/690' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587839 none C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 11, 14, 14, 14, 47, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 14, 46, 46, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587839 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 Building ZINC001721587839 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721587839 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 689) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721587839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721587839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587839 none C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 13, 16, 16, 16, 46, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 16, 44, 44, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 690) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721587839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721587839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721587839 none C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 11, 14, 14, 14, 47, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 14, 46, 46, 50, 50, 50, 50, 50, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721587839 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721587839 Building ZINC001721588114 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721588114 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/691 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721588114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721588114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721588114 none C[C@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 10, 24, 24, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 44, 44, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/692 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/692' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721588114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721588114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721588114 none C[C@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 23, 23, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 41, 41, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721588114 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 Building ZINC001721588114 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721588114 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 691) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721588114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721588114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721588114 none C[C@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 10, 24, 24, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 44, 44, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 692) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721588114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721588114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721588114 none C[C@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 23, 23, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 41, 41, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721588114 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588114 Building ZINC001721588115 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721588115 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/693 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721588115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721588115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721588115 none C[C@@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 23, 23, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 41, 41, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/694 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721588115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721588115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721588115 none C[C@@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 10, 24, 24, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 44, 44, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721588115 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 Building ZINC001721588115 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721588115 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 693) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721588115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721588115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721588115 none C[C@@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 23, 23, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 41, 41, 50, 50, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 694) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721588115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721588115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721588115 none C[C@@H](CNC(=O)c1cnc2cccnn21)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 10, 24, 24, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 44, 44, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721588115 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721588115 Building ZINC001721625517 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721625517 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/695 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721625517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721625517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721625517 none CC(C)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 24, 24, 20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 33, 33, 33, 47, 47, 47, 47, 47, 48, 48, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 47, 47, 48, 48] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/696 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721625517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721625517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721625517 none CC(C)C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 33, 33, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 33, 33, 33, 46, 46, 46, 46, 46, 48, 48, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 46, 46, 48, 48] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 224 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721625517 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 Building ZINC001721625517 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721625517 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 695) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721625517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721625517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721625517 none CC(C)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 24, 24, 20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 33, 33, 33, 47, 47, 47, 47, 47, 48, 48, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 47, 47, 48, 48] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 696) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721625517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721625517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721625517 none CC(C)C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 33, 33, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 33, 33, 33, 46, 46, 46, 46, 46, 48, 48, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 46, 46, 48, 48] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 224 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721625517 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625517 Building ZINC001721625518 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721625518 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/697 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721625518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721625518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721625518 none CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 23, 12, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 29, 40, 40, 40, 40, 40, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 40, 40, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 220 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/698 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721625518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721625518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721625518 none CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 32, 32, 32, 49, 49, 49, 49, 49, 50, 50, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 49, 49, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 239 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721625518 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 Building ZINC001721625518 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721625518 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 697) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721625518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721625518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721625518 none CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 23, 12, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 29, 40, 40, 40, 40, 40, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 40, 40, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 220 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 698) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001721625518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721625518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721625518 none CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 32, 32, 32, 49, 49, 49, 49, 49, 50, 50, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 49, 49, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 239 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721625518 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721625518 Building ZINC001721627781 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721627781 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/699 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C(N)=O)C1CCCCC1) `ZINC001721627781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721627781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721627781 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C(N)=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 17, 32, 32, 32, 40, 40, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 32, 40, 40, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/700 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C(N)=O)C1CCCCC1) `ZINC001721627781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721627781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721627781 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C(N)=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 15, 29, 29, 29, 39, 39, 8, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 29, 39, 39, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721627781 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 Building ZINC001721627781 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721627781 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 699) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C(N)=O)C1CCCCC1) `ZINC001721627781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721627781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721627781 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C(N)=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 17, 32, 32, 32, 40, 40, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 32, 40, 40, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 700) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C(N)=O)C1CCCCC1) `ZINC001721627781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721627781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721627781 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C(N)=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 15, 29, 29, 29, 39, 39, 8, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 29, 39, 39, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721627781 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627781 Building ZINC001721627782 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721627782 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/701 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C(N)=O)C1CCCCC1) `ZINC001721627782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721627782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721627782 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C(N)=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 15, 32, 32, 32, 39, 39, 9, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 32, 39, 39, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/702 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C(N)=O)C1CCCCC1) `ZINC001721627782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721627782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721627782 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C(N)=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 16, 33, 33, 33, 41, 41, 6, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 33, 41, 41, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721627782 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 Building ZINC001721627782 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721627782 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 701) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C(N)=O)C1CCCCC1) `ZINC001721627782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721627782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721627782 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C(N)=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 15, 32, 32, 32, 39, 39, 9, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 32, 39, 39, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 702) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C(N)=O)C1CCCCC1) `ZINC001721627782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721627782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721627782 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C(N)=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 16, 33, 33, 33, 41, 41, 6, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 33, 41, 41, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721627782 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721627782 Building ZINC001721634168 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721634168 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/703 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCNC(=O)Cn1cncn1) `ZINC001721634168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721634168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721634168 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 7, 12, 12, 12, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 12, 39, 39, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/704 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCNC(=O)Cn1cncn1) `ZINC001721634168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721634168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721634168 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 6, 10, 10, 10, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 6, 6, 10, 36, 36, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721634168 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 Building ZINC001721634168 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721634168 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 703) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCNC(=O)Cn1cncn1) `ZINC001721634168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721634168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721634168 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 7, 12, 12, 12, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 12, 39, 39, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 704) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCNC(=O)Cn1cncn1) `ZINC001721634168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721634168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721634168 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 6, 10, 10, 10, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 6, 6, 10, 36, 36, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721634168 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634168 Building ZINC001721634169 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721634169 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/705 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCNC(=O)Cn1cncn1) `ZINC001721634169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721634169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721634169 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 6, 10, 10, 10, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 6, 6, 10, 36, 36, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/706 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/706' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCNC(=O)Cn1cncn1) `ZINC001721634169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721634169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721634169 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 7, 12, 12, 12, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 12, 39, 39, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721634169 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 Building ZINC001721634169 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721634169 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 705) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCNC(=O)Cn1cncn1) `ZINC001721634169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721634169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721634169 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 6, 10, 10, 10, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 6, 6, 10, 36, 36, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 706) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCNC(=O)Cn1cncn1) `ZINC001721634169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721634169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721634169 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 7, 12, 12, 12, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 12, 39, 39, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721634169 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721634169 Building ZINC001721644084 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721644084 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/707 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H](C)[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721644084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721644084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644084 none CC(=O)NCC(=O)N1CCC[C@H](C)[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 39, 26, 39, 26, 26, 26, 26, 26, 26, 26, 17, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/708 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H](C)[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721644084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721644084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644084 none CC(=O)NCC(=O)N1CCC[C@H](C)[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 36, 26, 36, 26, 26, 26, 26, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721644084 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 Building ZINC001721644084 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721644084 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 707) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H](C)[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721644084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721644084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644084 none CC(=O)NCC(=O)N1CCC[C@H](C)[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 39, 26, 39, 26, 26, 26, 26, 26, 26, 26, 17, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 708) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H](C)[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721644084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721644084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644084 none CC(=O)NCC(=O)N1CCC[C@H](C)[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 36, 26, 36, 26, 26, 26, 26, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721644084 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644084 Building ZINC001721644085 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721644085 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/709 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H](C)[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721644085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721644085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644085 none CC(=O)NCC(=O)N1CCC[C@@H](C)[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 37, 26, 37, 26, 26, 26, 26, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/710 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H](C)[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721644085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721644085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644085 none CC(=O)NCC(=O)N1CCC[C@@H](C)[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 39, 26, 39, 26, 26, 26, 26, 26, 26, 26, 17, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721644085 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 Building ZINC001721644085 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721644085 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 709) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H](C)[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721644085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721644085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644085 none CC(=O)NCC(=O)N1CCC[C@@H](C)[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 37, 26, 37, 26, 26, 26, 26, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 710) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H](C)[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721644085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721644085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644085 none CC(=O)NCC(=O)N1CCC[C@@H](C)[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 39, 26, 39, 26, 26, 26, 26, 26, 26, 26, 17, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721644085 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644085 Building ZINC001721644086 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721644086 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/711 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H](C)[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721644086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721644086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644086 none CC(=O)NCC(=O)N1CCC[C@H](C)[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 36, 29, 36, 29, 29, 29, 29, 29, 29, 29, 15, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 46, 46, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/712 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H](C)[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721644086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721644086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644086 none CC(=O)NCC(=O)N1CCC[C@H](C)[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 29, 19, 29, 19, 19, 19, 19, 19, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 45, 45, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721644086 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 Building ZINC001721644086 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721644086 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 711) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H](C)[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721644086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721644086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644086 none CC(=O)NCC(=O)N1CCC[C@H](C)[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 36, 29, 36, 29, 29, 29, 29, 29, 29, 29, 15, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 46, 46, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 712) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H](C)[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721644086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721644086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644086 none CC(=O)NCC(=O)N1CCC[C@H](C)[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 29, 19, 29, 19, 19, 19, 19, 19, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 45, 45, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721644086 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644086 Building ZINC001721644087 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721644087 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/713 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H](C)[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721644087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721644087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644087 none CC(=O)NCC(=O)N1CCC[C@@H](C)[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 36, 28, 36, 28, 28, 28, 28, 28, 28, 28, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 46, 46, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/714 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/714' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H](C)[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721644087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721644087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644087 none CC(=O)NCC(=O)N1CCC[C@@H](C)[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 36, 28, 36, 28, 28, 28, 28, 28, 28, 28, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 47, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 188 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721644087 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 Building ZINC001721644087 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721644087 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 713) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H](C)[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721644087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721644087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644087 none CC(=O)NCC(=O)N1CCC[C@@H](C)[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 36, 28, 36, 28, 28, 28, 28, 28, 28, 28, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 46, 46, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 714) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H](C)[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721644087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721644087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721644087 none CC(=O)NCC(=O)N1CCC[C@@H](C)[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 36, 28, 36, 28, 28, 28, 28, 28, 28, 28, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 47, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 188 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721644087 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721644087 Building ZINC001721660925 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721660925 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/715 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1) `ZINC001721660925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721660925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721660925 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 9, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 20, 20, 20, 43, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/716 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1) `ZINC001721660925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721660925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721660925 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 11, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 22, 46, 49, 49, 49, 49, 22, 22, 22, 22, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 46, 46, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721660925 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 Building ZINC001721660925 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721660925 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 715) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1) `ZINC001721660925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721660925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721660925 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 9, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 20, 20, 20, 43, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 716) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1) `ZINC001721660925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721660925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721660925 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 11, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 22, 46, 49, 49, 49, 49, 22, 22, 22, 22, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 46, 46, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721660925 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660925 Building ZINC001721660926 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721660926 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/717 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1) `ZINC001721660926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721660926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721660926 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 11, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 22, 46, 49, 49, 49, 49, 22, 22, 22, 22, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 46, 46, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/718 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1) `ZINC001721660926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721660926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721660926 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 21, 21, 21, 43, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721660926 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 Building ZINC001721660926 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721660926 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 717) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1) `ZINC001721660926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721660926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721660926 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 11, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 22, 46, 49, 49, 49, 49, 22, 22, 22, 22, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 46, 46, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 718) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1) `ZINC001721660926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721660926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721660926 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 21, 21, 21, 43, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721660926 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721660926 Building ZINC001721661145 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721661145 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/719 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1) `ZINC001721661145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721661145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721661145 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 19, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 20, 20, 20, 33, 34, 49, 49, 49, 49, 49, 19, 19, 19, 19, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 33, 33, 34, 34, 49] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/720 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/720' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1) `ZINC001721661145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721661145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721661145 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 18, 23, 11, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 23, 23, 33, 33, 48, 48, 48, 48, 48, 23, 23, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 33, 33, 33, 33, 48] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 203 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721661145 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 Building ZINC001721661145 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721661145 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 719) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1) `ZINC001721661145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721661145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721661145 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 19, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 20, 20, 20, 33, 34, 49, 49, 49, 49, 49, 19, 19, 19, 19, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 33, 33, 34, 34, 49] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 720) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1) `ZINC001721661145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721661145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721661145 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 18, 23, 11, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 23, 23, 33, 33, 48, 48, 48, 48, 48, 23, 23, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 33, 33, 33, 33, 48] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 203 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721661145 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661145 Building ZINC001721661146 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721661146 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/721 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1) `ZINC001721661146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721661146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721661146 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 22, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 22, 34, 34, 49, 49, 49, 49, 49, 22, 22, 22, 22, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 34, 34, 34, 34, 49] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/722 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1) `ZINC001721661146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721661146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721661146 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 20, 11, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 21, 21, 21, 33, 34, 49, 49, 49, 49, 49, 20, 20, 20, 20, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 33, 33, 34, 34, 49] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721661146 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 Building ZINC001721661146 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721661146 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 721) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1) `ZINC001721661146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721661146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721661146 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 22, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 22, 34, 34, 49, 49, 49, 49, 49, 22, 22, 22, 22, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 34, 34, 34, 34, 49] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 722) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1) `ZINC001721661146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721661146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721661146 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 20, 11, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 21, 21, 21, 33, 34, 49, 49, 49, 49, 49, 20, 20, 20, 20, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 33, 33, 34, 34, 49] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721661146 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661146 Building ZINC001721661273 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721661273 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/723 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1) `ZINC001721661273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721661273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721661273 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 11, 7, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 40, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/724 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1) `ZINC001721661273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721661273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721661273 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 40, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721661273 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 Building ZINC001721661273 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721661273 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 723) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1) `ZINC001721661273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721661273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721661273 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 11, 7, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 40, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 724) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1) `ZINC001721661273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721661273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721661273 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 40, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721661273 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661273 Building ZINC001721661274 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721661274 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/725 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1) `ZINC001721661274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721661274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721661274 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 40, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/726 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1) `ZINC001721661274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721661274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721661274 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 15, 41, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721661274 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 Building ZINC001721661274 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721661274 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 725) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1) `ZINC001721661274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721661274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721661274 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 40, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 726) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1) `ZINC001721661274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721661274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721661274 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 15, 41, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721661274 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721661274 Building ZINC001721663879 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721663879 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/727 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O) `ZINC001721663879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721663879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721663879 none Cc1[nH]nc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 44, 44, 44, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 19, 19, 47, 47, 47, 47, 47, 44, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 141] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 356 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/728 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O) `ZINC001721663879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721663879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721663879 none Cc1[nH]nc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 40, 40, 40, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 20, 20, 44, 44, 44, 44, 44, 40, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 132] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 347 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721663879 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 Building ZINC001721663879 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721663879 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 727) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O) `ZINC001721663879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721663879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721663879 none Cc1[nH]nc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 44, 44, 44, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 19, 19, 47, 47, 47, 47, 47, 44, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 141] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 356 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 728) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O) `ZINC001721663879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721663879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721663879 none Cc1[nH]nc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 40, 40, 40, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 20, 20, 44, 44, 44, 44, 44, 40, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 132] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 347 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721663879 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663879 Building ZINC001721663880 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721663880 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/729 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O) `ZINC001721663880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721663880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721663880 none Cc1[nH]nc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 40, 40, 40, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 20, 20, 44, 44, 44, 44, 44, 40, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 132] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 347 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/730 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O) `ZINC001721663880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721663880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721663880 none Cc1[nH]nc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 44, 44, 44, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 19, 19, 47, 47, 47, 47, 47, 44, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 141] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 356 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721663880 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 Building ZINC001721663880 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721663880 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 729) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O) `ZINC001721663880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721663880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721663880 none Cc1[nH]nc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 40, 40, 40, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 20, 20, 44, 44, 44, 44, 44, 40, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 132] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 347 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 730) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O) `ZINC001721663880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721663880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721663880 none Cc1[nH]nc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 44, 44, 44, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 19, 19, 47, 47, 47, 47, 47, 44, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 141] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 356 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721663880 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721663880 Building ZINC001721665425 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721665425 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/731 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721665425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721665425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721665425 none CC(C)[C@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 2, 5, 5, 16, 27, 27, 27, 49, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 16, 16, 27, 49, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/732 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721665425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721665425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721665425 none CC(C)[C@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 2, 5, 5, 16, 29, 29, 29, 45, 45, 45, 45, 45, 45, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 29, 45, 45, 45, 45, 45, 45, 45, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721665425 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 Building ZINC001721665425 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721665425 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 731) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721665425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721665425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721665425 none CC(C)[C@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 2, 5, 5, 16, 27, 27, 27, 49, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 16, 16, 27, 49, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 732) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721665425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721665425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721665425 none CC(C)[C@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 2, 5, 5, 16, 29, 29, 29, 45, 45, 45, 45, 45, 45, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 29, 45, 45, 45, 45, 45, 45, 45, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721665425 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665425 Building ZINC001721665426 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721665426 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/733 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721665426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721665426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721665426 none CC(C)[C@@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 2, 5, 5, 13, 29, 29, 29, 47, 47, 47, 47, 47, 47, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 13, 13, 29, 47, 47, 47, 47, 47, 47, 47, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/734 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721665426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721665426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721665426 none CC(C)[C@@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 2, 5, 5, 13, 27, 27, 27, 47, 48, 48, 48, 47, 47, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 13, 13, 27, 48, 48, 48, 47, 47, 47, 47, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721665426 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 Building ZINC001721665426 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721665426 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 733) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721665426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721665426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721665426 none CC(C)[C@@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 2, 5, 5, 13, 29, 29, 29, 47, 47, 47, 47, 47, 47, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 13, 13, 29, 47, 47, 47, 47, 47, 47, 47, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 734) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721665426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721665426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721665426 none CC(C)[C@@H](CNC(=O)C1(NC(N)=O)CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 2, 5, 5, 13, 27, 27, 27, 47, 48, 48, 48, 47, 47, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 13, 13, 27, 48, 48, 48, 47, 47, 47, 47, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721665426 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721665426 Building ZINC001721669365 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721669365 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/735 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721669365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721669365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669365 none CC(C)[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 2, 4, 4, 10, 15, 15, 15, 37, 48, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 10, 10, 15, 37, 37, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/736 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721669365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721669365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669365 none CC(C)[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 6, 6, 13, 19, 19, 19, 40, 49, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 13, 13, 19, 40, 40, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721669365 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 Building ZINC001721669365 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721669365 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 735) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721669365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721669365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669365 none CC(C)[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 2, 4, 4, 10, 15, 15, 15, 37, 48, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 10, 10, 15, 37, 37, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 736) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721669365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721669365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669365 none CC(C)[C@@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 6, 6, 13, 19, 19, 19, 40, 49, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 13, 13, 19, 40, 40, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721669365 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669365 Building ZINC001721669366 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721669366 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/737 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721669366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721669366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669366 none CC(C)[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 2, 6, 6, 12, 16, 16, 16, 39, 49, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 12, 12, 16, 39, 39, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/738 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721669366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721669366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669366 none CC(C)[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 2, 4, 4, 7, 15, 15, 15, 38, 48, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 7, 7, 15, 38, 38, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721669366 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 Building ZINC001721669366 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721669366 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 737) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721669366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721669366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669366 none CC(C)[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 2, 6, 6, 12, 16, 16, 16, 39, 49, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 12, 12, 16, 39, 39, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 738) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721669366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721669366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669366 none CC(C)[C@H](CNC(=O)CO[C@@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 2, 4, 4, 7, 15, 15, 15, 38, 48, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 7, 7, 15, 38, 38, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721669366 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669366 Building ZINC001721669367 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721669367 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/739 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721669367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721669367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669367 none CC(C)[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 2, 4, 4, 7, 15, 15, 15, 37, 49, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 7, 7, 15, 37, 37, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/740 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721669367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721669367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669367 none CC(C)[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 2, 5, 5, 11, 15, 15, 15, 41, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 11, 11, 15, 41, 41, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721669367 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 Building ZINC001721669367 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721669367 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 739) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721669367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721669367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669367 none CC(C)[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 2, 4, 4, 7, 15, 15, 15, 37, 49, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 7, 7, 15, 37, 37, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 740) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721669367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721669367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669367 none CC(C)[C@@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 2, 5, 5, 11, 15, 15, 15, 41, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 11, 11, 15, 41, 41, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721669367 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669367 Building ZINC001721669368 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721669368 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/741 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721669368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721669368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669368 none CC(C)[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 6, 6, 13, 18, 18, 18, 40, 48, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 13, 13, 18, 40, 40, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/742 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721669368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721669368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669368 none CC(C)[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 2, 4, 4, 9, 16, 16, 16, 37, 47, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 9, 9, 16, 37, 37, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721669368 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 Building ZINC001721669368 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721669368 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 741) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721669368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721669368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669368 none CC(C)[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 6, 6, 13, 18, 18, 18, 40, 48, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 13, 13, 18, 40, 40, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 742) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721669368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721669368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721669368 none CC(C)[C@H](CNC(=O)CO[C@H]1CCOC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 2, 4, 4, 9, 16, 16, 16, 37, 47, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 9, 9, 16, 37, 37, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721669368 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721669368 Building ZINC001721678603 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721678603 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/743 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721678603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721678603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678603 none CC(C)[C@@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 2, 5, 5, 11, 28, 28, 28, 42, 42, 42, 42, 42, 42, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 11, 11, 28, 42, 42, 42, 42, 42, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/744 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721678603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721678603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678603 none CC(C)[C@@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 2, 5, 5, 16, 33, 33, 33, 46, 46, 46, 46, 46, 46, 46, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 16, 16, 33, 46, 46, 46, 46, 46, 46, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721678603 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 Building ZINC001721678603 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721678603 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 743) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721678603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721678603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678603 none CC(C)[C@@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 2, 5, 5, 11, 28, 28, 28, 42, 42, 42, 42, 42, 42, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 11, 11, 28, 42, 42, 42, 42, 42, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 744) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721678603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721678603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678603 none CC(C)[C@@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 2, 5, 5, 16, 33, 33, 33, 46, 46, 46, 46, 46, 46, 46, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 16, 16, 33, 46, 46, 46, 46, 46, 46, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721678603 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678603 Building ZINC001721678604 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721678604 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/745 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721678604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721678604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678604 none CC(C)[C@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 13, 2, 5, 5, 14, 32, 32, 32, 46, 46, 46, 46, 46, 46, 46, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 14, 14, 32, 46, 46, 46, 46, 46, 46, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/746 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721678604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721678604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678604 none CC(C)[C@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 2, 5, 5, 11, 28, 28, 28, 42, 42, 42, 42, 42, 42, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 11, 11, 28, 42, 42, 42, 42, 42, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721678604 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 Building ZINC001721678604 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721678604 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 745) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721678604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721678604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678604 none CC(C)[C@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 13, 2, 5, 5, 14, 32, 32, 32, 46, 46, 46, 46, 46, 46, 46, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 14, 14, 32, 46, 46, 46, 46, 46, 46, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 746) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721678604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721678604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678604 none CC(C)[C@H](CNC(=O)c1cn(C)ccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 2, 5, 5, 11, 28, 28, 28, 42, 42, 42, 42, 42, 42, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 11, 11, 28, 42, 42, 42, 42, 42, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721678604 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678604 Building ZINC001721678917 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721678917 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/747 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721678917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721678917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678917 none CC(C)[C@@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 2, 5, 5, 13, 28, 28, 28, 39, 39, 39, 39, 39, 39, 39, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 13, 13, 28, 39, 39, 39, 39, 39, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/748 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721678917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721678917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678917 none CC(C)[C@@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 2, 4, 4, 13, 29, 29, 29, 49, 49, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 13, 13, 29, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721678917 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 Building ZINC001721678917 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721678917 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 747) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721678917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721678917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678917 none CC(C)[C@@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 2, 5, 5, 13, 28, 28, 28, 39, 39, 39, 39, 39, 39, 39, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 13, 13, 28, 39, 39, 39, 39, 39, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 748) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721678917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721678917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678917 none CC(C)[C@@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 2, 4, 4, 13, 29, 29, 29, 49, 49, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 13, 13, 29, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721678917 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678917 Building ZINC001721678918 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721678918 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/749 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721678918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721678918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678918 none CC(C)[C@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 2, 4, 4, 13, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 13, 13, 30, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/750 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721678918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721678918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678918 none CC(C)[C@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 2, 5, 5, 13, 29, 29, 29, 39, 39, 39, 39, 39, 39, 39, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 13, 13, 29, 39, 39, 39, 39, 39, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721678918 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 Building ZINC001721678918 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721678918 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 749) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721678918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721678918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678918 none CC(C)[C@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 2, 4, 4, 13, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 13, 13, 30, 49, 49, 49, 49, 49, 49, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 750) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721678918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721678918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721678918 none CC(C)[C@H](CNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 2, 5, 5, 13, 29, 29, 29, 39, 39, 39, 39, 39, 39, 39, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 13, 13, 29, 39, 39, 39, 39, 39, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721678918 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721678918 Building ZINC001721682581 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721682581 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/751 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721682581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721682581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721682581 none CC(C)[C@@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 2, 4, 4, 7, 14, 14, 14, 24, 23, 23, 42, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 7, 7, 14, 24, 42, 42, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/752 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721682581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721682581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721682581 none CC(C)[C@@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 2, 3, 3, 7, 16, 16, 16, 20, 20, 20, 36, 48, 48, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 7, 7, 16, 20, 36, 36, 48, 48, 48, 48, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721682581 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 Building ZINC001721682581 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721682581 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 751) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721682581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721682581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721682581 none CC(C)[C@@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 2, 4, 4, 7, 14, 14, 14, 24, 23, 23, 42, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 7, 7, 14, 24, 42, 42, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 752) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721682581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721682581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721682581 none CC(C)[C@@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 2, 3, 3, 7, 16, 16, 16, 20, 20, 20, 36, 48, 48, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 7, 7, 16, 20, 36, 36, 48, 48, 48, 48, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721682581 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682581 Building ZINC001721682582 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721682582 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/753 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721682582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721682582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721682582 none CC(C)[C@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 2, 3, 3, 7, 18, 18, 18, 22, 22, 22, 39, 48, 48, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 7, 7, 18, 22, 39, 39, 48, 48, 48, 48, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/754 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721682582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721682582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721682582 none CC(C)[C@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 2, 4, 4, 9, 15, 15, 15, 24, 23, 23, 40, 47, 47, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 9, 9, 15, 24, 40, 40, 47, 47, 47, 47, 47, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721682582 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 Building ZINC001721682582 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721682582 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 753) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721682582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721682582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721682582 none CC(C)[C@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 2, 3, 3, 7, 18, 18, 18, 22, 22, 22, 39, 48, 48, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 7, 7, 18, 22, 39, 39, 48, 48, 48, 48, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 754) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721682582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721682582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721682582 none CC(C)[C@H](CNC(=O)C(=O)NCC1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 2, 4, 4, 9, 15, 15, 15, 24, 23, 23, 40, 47, 47, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 9, 9, 15, 24, 40, 40, 47, 47, 47, 47, 47, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721682582 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721682582 Building ZINC001721694243 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721694243 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/755 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O) `ZINC001721694243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721694243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721694243 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 15, 33, 33, 42, 50, 50, 50, 50, 50, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/756 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O) `ZINC001721694243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721694243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721694243 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 15, 34, 34, 42, 50, 50, 50, 50, 50, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721694243 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 Building ZINC001721694243 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721694243 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 755) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O) `ZINC001721694243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721694243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721694243 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 15, 33, 33, 42, 50, 50, 50, 50, 50, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 756) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O) `ZINC001721694243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721694243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721694243 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 15, 34, 34, 42, 50, 50, 50, 50, 50, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721694243 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721694243 Building ZINC001721699309 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699309 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/757 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1ccccc1=O) `ZINC001721699309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699309 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 34, 34, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/758 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1ccccc1=O) `ZINC001721699309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699309 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 32, 32, 34, 34, 50, 50, 50, 50, 50, 50, 21, 21, 21, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699309 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 Building ZINC001721699309 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699309 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 757) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1ccccc1=O) `ZINC001721699309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699309 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 34, 34, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 758) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1ccccc1=O) `ZINC001721699309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699309 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 32, 32, 34, 34, 50, 50, 50, 50, 50, 50, 21, 21, 21, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699309 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699309 Building ZINC001721699350 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699350 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/759 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699350 none CC(=O)N1CCC[C@@H]1C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 50, 26, 40, 9, 26, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/760 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699350 none CC(=O)N1CCC[C@@H]1C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 45, 50, 29, 43, 12, 29, 10, 4, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 12, 12, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699350 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 Building ZINC001721699350 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699350 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 759) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699350 none CC(=O)N1CCC[C@@H]1C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 50, 26, 40, 9, 26, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 760) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699350 none CC(=O)N1CCC[C@@H]1C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 45, 50, 29, 43, 12, 29, 10, 4, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 12, 12, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699350 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699350 Building ZINC001721699395 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699395 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/761 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1) `ZINC001721699395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699395 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 43, 43, 46, 46, 46, 50, 50, 46, 46, 46, 21, 21, 21, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 50, 50, 46, 46] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/762 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1) `ZINC001721699395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699395 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 23, 42, 42, 45, 45, 45, 50, 50, 45, 45, 45, 23, 23, 23, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 45, 45] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699395 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 Building ZINC001721699395 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699395 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 761) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1) `ZINC001721699395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699395 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 43, 43, 46, 46, 46, 50, 50, 46, 46, 46, 21, 21, 21, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 50, 50, 46, 46] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 762) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1) `ZINC001721699395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699395 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 23, 42, 42, 45, 45, 45, 50, 50, 45, 45, 45, 23, 23, 23, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 45, 45] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699395 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699395 Building ZINC001721699406 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699406 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/763 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]1(C)CNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699406 none CN(CCN(C)C(=O)[C@]1(C)CNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 12, 31, 31, 44, 45, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 12, 12, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 177 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/764 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]1(C)CNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699406 none CN(CCN(C)C(=O)[C@]1(C)CNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 12, 31, 31, 45, 45, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 12, 12, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699406 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 Building ZINC001721699406 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699406 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 763) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]1(C)CNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699406 none CN(CCN(C)C(=O)[C@]1(C)CNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 12, 31, 31, 44, 45, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 12, 12, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 177 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 764) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]1(C)CNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699406 none CN(CCN(C)C(=O)[C@]1(C)CNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 12, 31, 31, 45, 45, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 12, 12, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699406 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699406 Building ZINC001721699407 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699407 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/765 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]1(C)CNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699407 none CN(CCN(C)C(=O)[C@@]1(C)CNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 14, 36, 36, 48, 48, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 14, 14, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/766 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]1(C)CNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699407 none CN(CCN(C)C(=O)[C@@]1(C)CNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 13, 34, 34, 49, 49, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 13, 13, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699407 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 Building ZINC001721699407 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699407 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 765) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]1(C)CNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699407 none CN(CCN(C)C(=O)[C@@]1(C)CNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 14, 36, 36, 48, 48, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 14, 14, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 766) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]1(C)CNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699407 none CN(CCN(C)C(=O)[C@@]1(C)CNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 13, 34, 34, 49, 49, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 13, 13, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699407 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699407 Building ZINC001721699445 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699445 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/767 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699445 none CN(CCN(C)C(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 10, 20, 20, 22, 36, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/768 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699445 none CN(CCN(C)C(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 10, 18, 18, 20, 37, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699445 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 Building ZINC001721699445 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699445 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 767) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699445 none CN(CCN(C)C(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 10, 20, 20, 22, 36, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 768) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699445 none CN(CCN(C)C(=O)[C@@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 10, 18, 18, 20, 37, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699445 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699445 Building ZINC001721699446 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699446 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/769 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699446 none CN(CCN(C)C(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 13, 13, 24, 24, 29, 39, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 156 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/770 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699446 none CN(CCN(C)C(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 13, 13, 24, 24, 30, 41, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 154 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699446 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 Building ZINC001721699446 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699446 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 769) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699446 none CN(CCN(C)C(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 13, 13, 24, 24, 29, 39, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 156 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 770) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721699446 none CN(CCN(C)C(=O)[C@]1(C)CCNC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 13, 13, 24, 24, 30, 41, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 154 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699446 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699446 Building ZINC001721699448 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699448 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/771 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001721699448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699448 none Cc1cc(OCC(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 20, 15, 20, 7, 15, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/772 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001721699448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699448 none Cc1cc(OCC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 20, 15, 20, 7, 15, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699448 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 Building ZINC001721699448 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699448 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 771) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001721699448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699448 none Cc1cc(OCC(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 20, 15, 20, 7, 15, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 772) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001721699448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699448 none Cc1cc(OCC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 20, 15, 20, 7, 15, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699448 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699448 Building ZINC001721699518 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699518 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/773 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC1OCCCO1) `ZINC001721699518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721699518 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 33, 33, 33, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/774 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC1OCCCO1) `ZINC001721699518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721699518 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 35, 35, 36, 50, 50, 50, 50, 50, 21, 21, 21, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699518 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 Building ZINC001721699518 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699518 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 773) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC1OCCCO1) `ZINC001721699518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721699518 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 33, 33, 33, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 774) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC1OCCCO1) `ZINC001721699518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721699518 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 35, 35, 36, 50, 50, 50, 50, 50, 21, 21, 21, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699518 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699518 Building ZINC001721699538 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699538 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/775 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001721699538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699538 none COc1cnc(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 50, 50, 27, 20, 27, 11, 20, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 20, 20, 20, 11, 11, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/776 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001721699538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699538 none COc1cnc(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 50, 50, 27, 20, 27, 11, 20, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 20, 20, 20, 11, 11, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699538 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 Building ZINC001721699538 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699538 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 775) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001721699538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699538 none COc1cnc(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 50, 50, 27, 20, 27, 11, 20, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 20, 20, 20, 11, 11, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 776) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001721699538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699538 none COc1cnc(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 50, 50, 27, 20, 27, 11, 20, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 20, 20, 20, 11, 11, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699538 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699538 Building ZINC001721699551 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699551 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/777 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699551 none COCc1nocc1C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 27, 12, 9, 12, 6, 9, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 27, 9, 9, 9, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/778 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699551 none COCc1nocc1C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 25, 25, 25, 25, 10, 7, 10, 6, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 25, 7, 7, 7, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699551 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 Building ZINC001721699551 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699551 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 777) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721699551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699551 none COCc1nocc1C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 27, 12, 9, 12, 6, 9, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 27, 9, 9, 9, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 778) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721699551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699551 none COCc1nocc1C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 25, 25, 25, 25, 10, 7, 10, 6, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 25, 7, 7, 7, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699551 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699551 Building ZINC001721699582 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699582 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/779 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21) `ZINC001721699582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699582 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 14, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 6, 6, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/780 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21) `ZINC001721699582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699582 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 14, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 6, 6, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699582 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 Building ZINC001721699582 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699582 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 779) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21) `ZINC001721699582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699582 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 14, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 6, 6, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 780) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21) `ZINC001721699582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699582 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 14, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 6, 6, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699582 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699582 Building ZINC001721699647 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699647 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/781 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1) `ZINC001721699647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699647 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 33, 33, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/782 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1) `ZINC001721699647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699647 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 34, 34, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699647 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 Building ZINC001721699647 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699647 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 781) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1) `ZINC001721699647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699647 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 33, 33, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 782) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1) `ZINC001721699647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721699647 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 34, 34, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699647 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699647 Building ZINC001721699653 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699653 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/783 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCN1C(N)=O) `ZINC001721699653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699653 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCN1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/784 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCN1C(N)=O) `ZINC001721699653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699653 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCN1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 6, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 6, 6, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699653 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 Building ZINC001721699653 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699653 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 783) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCN1C(N)=O) `ZINC001721699653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699653 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCN1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 784) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCN1C(N)=O) `ZINC001721699653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699653 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCN1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 6, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 6, 6, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699653 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699653 Building ZINC001721699710 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699710 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/785 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001721699710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699710 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 41, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/786 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001721699710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699710 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 41, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699710 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 Building ZINC001721699710 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699710 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 785) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001721699710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699710 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 41, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 786) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001721699710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699710 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 41, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699710 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699710 Building ZINC001721699711 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699711 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/787 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001721699711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699711 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 41, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/788 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001721699711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699711 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 42, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699711 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 Building ZINC001721699711 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699711 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 787) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001721699711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699711 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 41, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 788) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001721699711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699711 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 42, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699711 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699711 Building ZINC001721699731 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699731 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/789 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)c[nH]1) `ZINC001721699731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699731 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 13, 27, 27, 40, 40, 40, 50, 50, 40, 40, 40, 13, 13, 13, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 50, 40] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/790 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)c[nH]1) `ZINC001721699731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699731 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 25, 25, 41, 41, 41, 50, 50, 41, 41, 41, 11, 11, 11, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 50, 50, 41] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699731 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 Building ZINC001721699731 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699731 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 789) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)c[nH]1) `ZINC001721699731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699731 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 13, 27, 27, 40, 40, 40, 50, 50, 40, 40, 40, 13, 13, 13, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 50, 40] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 790) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)c[nH]1) `ZINC001721699731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699731 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 25, 25, 41, 41, 41, 50, 50, 41, 41, 41, 11, 11, 11, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 50, 50, 41] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699731 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699731 Building ZINC001721699756 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699756 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/791 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn2nnnc2c1) `ZINC001721699756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721699756 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn2nnnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/792 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn2nnnc2c1) `ZINC001721699756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721699756 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn2nnnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699756 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 Building ZINC001721699756 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699756 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 791) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn2nnnc2c1) `ZINC001721699756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721699756 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn2nnnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 792) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn2nnnc2c1) `ZINC001721699756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721699756 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccn2nnnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699756 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699756 Building ZINC001721699758 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699758 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/793 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C) `ZINC001721699758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699758 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 24, 24, 26, 26, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/794 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/794' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C) `ZINC001721699758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699758 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 24, 24, 26, 26, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699758 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 Building ZINC001721699758 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699758 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 793) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C) `ZINC001721699758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699758 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 24, 24, 26, 26, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 794) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C) `ZINC001721699758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699758 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 24, 24, 26, 26, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699758 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699758 Building ZINC001721699812 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699812 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/795 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1nc2ncccn2n1) `ZINC001721699812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721699812 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1nc2ncccn2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/796 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1nc2ncccn2n1) `ZINC001721699812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721699812 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1nc2ncccn2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699812 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 Building ZINC001721699812 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699812 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 795) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1nc2ncccn2n1) `ZINC001721699812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721699812 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1nc2ncccn2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 796) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1nc2ncccn2n1) `ZINC001721699812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721699812 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1nc2ncccn2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699812 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699812 Building ZINC001721699818 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699818 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/797 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncc(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001721699818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699818 none COc1ncc(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 50, 50, 40, 19, 40, 9, 19, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 19, 19, 19, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/798 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncc(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001721699818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699818 none COc1ncc(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 50, 50, 40, 20, 40, 9, 20, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 20, 20, 20, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699818 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 Building ZINC001721699818 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699818 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 797) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncc(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001721699818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699818 none COc1ncc(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 50, 50, 40, 19, 40, 9, 19, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 19, 19, 19, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 798) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncc(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001721699818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721699818 none COc1ncc(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 50, 50, 40, 20, 40, 9, 20, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 20, 20, 20, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699818 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699818 Building ZINC001721699858 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699858 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/799 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccncn1) `ZINC001721699858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699858 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 25, 25, 29, 29, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/800 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccncn1) `ZINC001721699858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699858 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 25, 25, 29, 29, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699858 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 Building ZINC001721699858 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699858 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 799) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccncn1) `ZINC001721699858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699858 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 25, 25, 29, 29, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 800) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccncn1) `ZINC001721699858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699858 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 25, 25, 29, 29, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699858 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699858 Building ZINC001721699887 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699887 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/801 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721699887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699887 none COc1c(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 31, 16, 31, 7, 16, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/802 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721699887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699887 none COc1c(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 15, 30, 7, 15, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699887 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 Building ZINC001721699887 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699887 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 801) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721699887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699887 none COc1c(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 31, 16, 31, 7, 16, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 802) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001721699887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721699887 none COc1c(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 15, 30, 7, 15, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699887 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699887 Building ZINC001721699894 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699894 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/803 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(CC2CC2)nn1) `ZINC001721699894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699894 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 10, 20, 20, 21, 21, 21, 46, 50, 50, 21, 21, 10, 10, 10, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/804 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(CC2CC2)nn1) `ZINC001721699894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699894 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 19, 19, 20, 20, 20, 46, 50, 50, 20, 20, 9, 9, 9, 5, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699894 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 Building ZINC001721699894 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721699894 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 803) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(CC2CC2)nn1) `ZINC001721699894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721699894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699894 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 10, 20, 20, 21, 21, 21, 46, 50, 50, 21, 21, 10, 10, 10, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 804) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(CC2CC2)nn1) `ZINC001721699894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721699894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721699894 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 19, 19, 20, 20, 20, 46, 50, 50, 20, 20, 9, 9, 9, 5, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721699894 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721699894 Building ZINC001721700045 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721700045 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/805 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCCn1cncn1) `ZINC001721700045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721700045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721700045 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 16, 16, 16, 23, 36, 50, 50, 50, 50, 11, 11, 11, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 23, 23, 36, 36, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/806 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCCn1cncn1) `ZINC001721700045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721700045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721700045 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 16, 16, 16, 23, 36, 50, 50, 50, 50, 11, 11, 11, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 23, 23, 36, 36, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721700045 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 Building ZINC001721700045 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721700045 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 805) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCCn1cncn1) `ZINC001721700045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721700045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721700045 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 16, 16, 16, 23, 36, 50, 50, 50, 50, 11, 11, 11, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 23, 23, 36, 36, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 806) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCCn1cncn1) `ZINC001721700045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721700045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721700045 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 16, 16, 16, 23, 36, 50, 50, 50, 50, 11, 11, 11, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 23, 23, 36, 36, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721700045 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721700045 Building ZINC001721726584 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721726584 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/807 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721726584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726584 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 31, 48, 48, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 31, 31, 48, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 277 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/808 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721726584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726584 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 26, 40, 40, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 26, 26, 40, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721726584 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 Building ZINC001721726584 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721726584 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 807) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721726584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726584 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 31, 48, 48, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 31, 31, 48, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 277 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 808) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721726584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726584 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 26, 40, 40, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 26, 26, 40, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721726584 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726584 Building ZINC001721726585 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721726585 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/809 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721726585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726585 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 26, 47, 47, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 26, 26, 47, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/810 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721726585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726585 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 26, 49, 49, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 26, 26, 49, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721726585 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 Building ZINC001721726585 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721726585 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 809) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721726585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726585 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 26, 47, 47, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 26, 26, 47, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 810) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721726585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726585 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 26, 49, 49, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 26, 26, 49, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721726585 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726585 Building ZINC001721726586 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721726586 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/811 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721726586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726586 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 26, 42, 42, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 26, 26, 42, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/812 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721726586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726586 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 31, 47, 47, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 31, 31, 47, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 277 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721726586 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 Building ZINC001721726586 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721726586 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 811) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721726586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726586 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 26, 42, 42, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 26, 26, 42, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 812) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721726586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726586 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 31, 47, 47, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 31, 31, 47, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 277 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721726586 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726586 Building ZINC001721726587 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721726587 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/813 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721726587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726587 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 25, 49, 49, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 25, 25, 49, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/814 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721726587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726587 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 27, 49, 49, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 27, 27, 49, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721726587 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 Building ZINC001721726587 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721726587 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 813) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721726587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726587 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 25, 49, 49, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 25, 25, 49, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 814) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1) `ZINC001721726587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721726587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721726587 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1ccc(O)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 27, 49, 49, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 27, 27, 49, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721726587 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721726587 Building ZINC001721728028 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721728028 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/815 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721728028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728028 none Cn1ncc(C(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 21, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 33, 21, 21, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 151 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/816 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721728028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728028 none Cn1ncc(C(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 37, 37, 25, 10, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 25, 25, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 167 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721728028 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 Building ZINC001721728028 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721728028 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 815) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721728028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728028 none Cn1ncc(C(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 21, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 33, 21, 21, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 151 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 816) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721728028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728028 none Cn1ncc(C(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 37, 37, 25, 10, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 25, 25, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 167 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721728028 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728028 Building ZINC001721728030 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721728030 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/817 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721728030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728030 none Cn1ncc(C(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 28, 28, 20, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 28, 20, 20, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 139 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/818 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721728030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728030 none Cn1ncc(C(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 22, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 33, 22, 22, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 145 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721728030 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 Building ZINC001721728030 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721728030 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 817) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721728030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728030 none Cn1ncc(C(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 28, 28, 20, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 28, 20, 20, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 139 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 818) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721728030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728030 none Cn1ncc(C(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 22, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 33, 22, 22, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 145 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721728030 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728030 Building ZINC001721728032 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721728032 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/819 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721728032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728032 none Cn1ncc(C(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 38, 38, 25, 10, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 38, 25, 25, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 165 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/820 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721728032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728032 none Cn1ncc(C(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 23, 12, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 23, 23, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 150 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721728032 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 Building ZINC001721728032 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721728032 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 819) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721728032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728032 none Cn1ncc(C(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 38, 38, 25, 10, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 38, 25, 25, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 165 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 820) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721728032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728032 none Cn1ncc(C(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 23, 12, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 23, 23, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 150 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721728032 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728032 Building ZINC001721728034 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721728034 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/821 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721728034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728034 none Cn1ncc(C(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 23, 10, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 23, 23, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 154 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/822 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721728034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728034 none Cn1ncc(C(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 27, 27, 20, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 27, 20, 20, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 135 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721728034 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 Building ZINC001721728034 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721728034 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 821) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721728034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728034 none Cn1ncc(C(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 23, 10, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 23, 23, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 154 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 822) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N) `ZINC001721728034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721728034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721728034 none Cn1ncc(C(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 27, 27, 20, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 27, 20, 20, 9, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 135 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721728034 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721728034 Building ZINC001721729024 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729024 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/823 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729024 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 33, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 33, 33, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/824 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729024 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 28, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 28, 28, 44, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729024 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 Building ZINC001721729024 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729024 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 823) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729024 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 33, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 33, 33, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 824) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729024 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 28, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 28, 28, 44, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729024 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729024 Building ZINC001721729025 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729025 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/825 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729025 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 29, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 29, 29, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/826 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729025 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 30, 30, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729025 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 Building ZINC001721729025 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729025 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 825) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729025 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 29, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 29, 29, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 826) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729025 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 30, 30, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729025 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729025 Building ZINC001721729026 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729026 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/827 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729026 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 27, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 27, 27, 44, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/828 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729026 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 33, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 33, 33, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729026 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 Building ZINC001721729026 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729026 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 827) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729026 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 27, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 27, 27, 44, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 828) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729026 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 33, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 33, 33, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729026 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729026 Building ZINC001721729027 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729027 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/829 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729027 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/830 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729027 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 29, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 11, 29, 29, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729027 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 Building ZINC001721729027 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729027 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 829) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729027 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 830) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1) `ZINC001721729027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721729027 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 29, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 11, 29, 29, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729027 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729027 Building ZINC001721729140 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729140 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/831 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O) `ZINC001721729140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729140 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 11, 15, 15, 15, 39, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 11, 11, 15, 39, 39, 49, 49, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/832 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O) `ZINC001721729140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729140 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 10, 15, 15, 15, 32, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 15, 32, 32, 44, 44, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729140 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 Building ZINC001721729140 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729140 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 831) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O) `ZINC001721729140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729140 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 11, 15, 15, 15, 39, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 11, 11, 15, 39, 39, 49, 49, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 832) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O) `ZINC001721729140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729140 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 10, 15, 15, 15, 32, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 15, 32, 32, 44, 44, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729140 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729140 Building ZINC001721729141 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729141 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/833 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O) `ZINC001721729141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729141 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 10, 21, 21, 21, 40, 48, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 21, 40, 40, 48, 48, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/834 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O) `ZINC001721729141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729141 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 12, 23, 23, 23, 44, 48, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 12, 12, 23, 44, 44, 48, 48, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729141 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 Building ZINC001721729141 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729141 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 833) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O) `ZINC001721729141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729141 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 10, 21, 21, 21, 40, 48, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 21, 40, 40, 48, 48, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 834) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O) `ZINC001721729141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729141 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 12, 23, 23, 23, 44, 48, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 12, 12, 23, 44, 44, 48, 48, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729141 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729141 Building ZINC001721729142 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729142 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/835 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)CCNC(N)=O) `ZINC001721729142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729142 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 9, 14, 14, 14, 30, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 9, 9, 14, 30, 30, 44, 44, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/836 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)CCNC(N)=O) `ZINC001721729142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729142 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 10, 15, 15, 15, 38, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 15, 38, 38, 49, 49, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729142 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 Building ZINC001721729142 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729142 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 835) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)CCNC(N)=O) `ZINC001721729142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729142 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 9, 14, 14, 14, 30, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 9, 9, 14, 30, 30, 44, 44, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 836) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)CCNC(N)=O) `ZINC001721729142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729142 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 10, 15, 15, 15, 38, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 15, 38, 38, 49, 49, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729142 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729142 Building ZINC001721729143 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729143 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/837 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)CCNC(N)=O) `ZINC001721729143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729143 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 11, 22, 22, 22, 43, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 11, 11, 22, 43, 43, 49, 49, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/838 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)CCNC(N)=O) `ZINC001721729143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729143 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 40, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 11, 11, 24, 40, 40, 49, 49, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729143 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 Building ZINC001721729143 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729143 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 837) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)CCNC(N)=O) `ZINC001721729143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729143 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 11, 22, 22, 22, 43, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 11, 11, 22, 43, 43, 49, 49, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 838) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)CCNC(N)=O) `ZINC001721729143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721729143 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 40, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 11, 11, 24, 40, 40, 49, 49, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729143 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729143 Building ZINC001721729416 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729416 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/839 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1) `ZINC001721729416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729416 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 10, 18, 18, 18, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 18, 40, 40, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/840 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1) `ZINC001721729416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729416 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 8, 12, 12, 12, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 8, 8, 12, 34, 34, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729416 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 Building ZINC001721729416 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729416 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 839) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1) `ZINC001721729416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729416 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 10, 18, 18, 18, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 18, 40, 40, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 840) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1) `ZINC001721729416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729416 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 8, 12, 12, 12, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 8, 8, 12, 34, 34, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729416 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729416 Building ZINC001721729417 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729417 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/841 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1) `ZINC001721729417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729417 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 12, 26, 26, 26, 45, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 12, 12, 26, 45, 45, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/842 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1) `ZINC001721729417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729417 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 6, 6, 6, 6, 6, 6, 10, 21, 21, 21, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 10, 10, 21, 39, 39, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729417 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 Building ZINC001721729417 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729417 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 841) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1) `ZINC001721729417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729417 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 12, 26, 26, 26, 45, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 12, 12, 26, 45, 45, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 842) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1) `ZINC001721729417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729417 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 6, 6, 6, 6, 6, 6, 10, 21, 21, 21, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 10, 10, 21, 39, 39, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729417 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729417 Building ZINC001721729418 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729418 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/843 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1ccnc1) `ZINC001721729418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729418 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 10, 20, 20, 20, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 10, 10, 20, 41, 41, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/844 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1ccnc1) `ZINC001721729418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729418 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 10, 23, 23, 23, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 10, 10, 23, 41, 41, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729418 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 Building ZINC001721729418 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729418 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 843) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1ccnc1) `ZINC001721729418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729418 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 10, 20, 20, 20, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 10, 10, 20, 41, 41, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 844) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1ccnc1) `ZINC001721729418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729418 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 10, 23, 23, 23, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 10, 10, 23, 41, 41, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729418 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729418 Building ZINC001721729419 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729419 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/845 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1ccnc1) `ZINC001721729419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729419 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 8, 12, 12, 12, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 8, 8, 12, 34, 34, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/846 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1ccnc1) `ZINC001721729419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729419 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 10, 19, 19, 19, 43, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 19, 43, 43, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729419 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 Building ZINC001721729419 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721729419 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 845) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1ccnc1) `ZINC001721729419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721729419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729419 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 8, 12, 12, 12, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 8, 8, 12, 34, 34, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 846) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1ccnc1) `ZINC001721729419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721729419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721729419 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 10, 19, 19, 19, 43, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 19, 43, 43, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721729419 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721729419 Building ZINC001721736556 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721736556 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/847 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)c1cncnc1O) `ZINC001721736556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721736556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736556 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 34, 34, 34, 34, 34, 44, 44, 44, 50, 50, 48, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 34, 34, 34, 34, 34, 34, 44, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 257 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/848 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)c1cncnc1O) `ZINC001721736556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721736556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736556 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 18, 32, 32, 32, 32, 32, 32, 32, 42, 42, 42, 50, 50, 49, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 13, 13, 32, 32, 32, 32, 32, 32, 42, 50, 50, 100] 100 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721736556 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 Building ZINC001721736556 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721736556 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 847) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)c1cncnc1O) `ZINC001721736556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721736556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736556 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 34, 34, 34, 34, 34, 34, 34, 44, 44, 44, 50, 50, 48, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 34, 34, 34, 34, 34, 34, 44, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 257 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 848) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)c1cncnc1O) `ZINC001721736556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721736556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736556 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 18, 32, 32, 32, 32, 32, 32, 32, 42, 42, 42, 50, 50, 49, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 13, 13, 32, 32, 32, 32, 32, 32, 42, 50, 50, 100] 100 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721736556 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736556 Building ZINC001721736557 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721736557 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/849 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)c1cncnc1O) `ZINC001721736557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721736557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736557 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 32, 32, 32, 32, 32, 32, 32, 40, 40, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 32, 32, 32, 32, 32, 32, 40, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 239 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/850 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)c1cncnc1O) `ZINC001721736557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721736557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736557 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 30, 30, 30, 30, 30, 30, 30, 40, 40, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 30, 30, 30, 30, 30, 40, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 244 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721736557 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 Building ZINC001721736557 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721736557 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 849) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)c1cncnc1O) `ZINC001721736557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721736557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736557 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 32, 32, 32, 32, 32, 32, 32, 40, 40, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 32, 32, 32, 32, 32, 32, 40, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 239 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 850) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)c1cncnc1O) `ZINC001721736557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721736557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736557 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 30, 30, 30, 30, 30, 30, 30, 40, 40, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 30, 30, 30, 30, 30, 40, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 244 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721736557 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736557 Building ZINC001721736558 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721736558 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/851 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)c1cncnc1O) `ZINC001721736558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721736558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736558 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 27, 27, 27, 27, 27, 27, 27, 36, 36, 36, 50, 50, 46, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 27, 27, 27, 27, 27, 27, 36, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 261 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/852 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)c1cncnc1O) `ZINC001721736558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721736558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736558 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 28, 28, 28, 28, 28, 28, 28, 41, 41, 41, 50, 50, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 28, 28, 28, 28, 28, 28, 41, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 252 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721736558 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 Building ZINC001721736558 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721736558 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 851) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)c1cncnc1O) `ZINC001721736558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721736558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736558 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 27, 27, 27, 27, 27, 27, 27, 36, 36, 36, 50, 50, 46, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 27, 27, 27, 27, 27, 27, 36, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 261 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 852) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)c1cncnc1O) `ZINC001721736558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721736558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736558 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 28, 28, 28, 28, 28, 28, 28, 41, 41, 41, 50, 50, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 28, 28, 28, 28, 28, 28, 41, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 252 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721736558 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736558 Building ZINC001721736559 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721736559 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/853 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)c1cncnc1O) `ZINC001721736559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721736559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736559 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 36, 36, 36, 36, 36, 36, 36, 45, 45, 45, 50, 50, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 36, 36, 36, 36, 36, 36, 45, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 256 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/854 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)c1cncnc1O) `ZINC001721736559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721736559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736559 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 37, 37, 37, 37, 37, 37, 37, 44, 44, 44, 50, 50, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 37, 37, 37, 37, 37, 37, 44, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 245 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721736559 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 Building ZINC001721736559 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721736559 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 853) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)c1cncnc1O) `ZINC001721736559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721736559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736559 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 36, 36, 36, 36, 36, 36, 36, 45, 45, 45, 50, 50, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 36, 36, 36, 36, 36, 36, 45, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 256 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 854) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)c1cncnc1O) `ZINC001721736559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721736559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721736559 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)c1cncnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 37, 37, 37, 37, 37, 37, 37, 44, 44, 44, 50, 50, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 37, 37, 37, 37, 37, 37, 44, 50, 50, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 245 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721736559 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721736559 Building ZINC001721741318 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721741318 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/855 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)Cc1cccs1) `ZINC001721741318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721741318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741318 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 9, 15, 15, 15, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 9, 9, 15, 36, 36, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/856 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)Cc1cccs1) `ZINC001721741318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721741318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741318 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 11, 16, 16, 16, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 11, 11, 16, 42, 42, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721741318 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 Building ZINC001721741318 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721741318 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 855) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)Cc1cccs1) `ZINC001721741318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721741318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741318 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 9, 15, 15, 15, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 9, 9, 15, 36, 36, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 856) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)Cc1cccs1) `ZINC001721741318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721741318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741318 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 11, 16, 16, 16, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 11, 11, 16, 42, 42, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721741318 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741318 Building ZINC001721741319 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721741319 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/857 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)Cc1cccs1) `ZINC001721741319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721741319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741319 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 11, 16, 16, 16, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 11, 11, 16, 41, 41, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/858 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)Cc1cccs1) `ZINC001721741319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721741319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741319 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 9, 15, 15, 15, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 9, 9, 15, 36, 36, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721741319 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 Building ZINC001721741319 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721741319 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 857) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)Cc1cccs1) `ZINC001721741319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721741319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741319 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 11, 16, 16, 16, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 11, 11, 16, 41, 41, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 858) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)Cc1cccs1) `ZINC001721741319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721741319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741319 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 9, 15, 15, 15, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 9, 9, 15, 36, 36, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721741319 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741319 Building ZINC001721741652 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721741652 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/859 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)s1) `ZINC001721741652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721741652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741652 none Cc1ccc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 48, 48, 33, 26, 11, 26, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 48, 33, 33, 78, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 288 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/860 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)s1) `ZINC001721741652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721741652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741652 none Cc1ccc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 48, 48, 37, 27, 9, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 48, 37, 37, 81, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 289 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721741652 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 Building ZINC001721741652 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721741652 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 859) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)s1) `ZINC001721741652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721741652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741652 none Cc1ccc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 48, 48, 33, 26, 11, 26, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 48, 33, 33, 78, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 288 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 860) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)s1) `ZINC001721741652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721741652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741652 none Cc1ccc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 48, 48, 37, 27, 9, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 48, 37, 37, 81, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 289 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721741652 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741652 Building ZINC001721741653 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721741653 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/861 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)s1) `ZINC001721741653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721741653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741653 none Cc1ccc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 49, 49, 49, 38, 28, 9, 28, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 49, 38, 38, 84, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 296 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/862 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)s1) `ZINC001721741653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721741653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741653 none Cc1ccc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 48, 48, 33, 26, 11, 26, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 48, 33, 33, 78, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 288 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721741653 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 Building ZINC001721741653 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721741653 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 861) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)s1) `ZINC001721741653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721741653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741653 none Cc1ccc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 49, 49, 49, 38, 28, 9, 28, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 49, 38, 38, 84, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 296 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 862) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)s1) `ZINC001721741653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721741653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721741653 none Cc1ccc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 48, 48, 33, 26, 11, 26, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 48, 33, 33, 78, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 288 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721741653 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721741653 Building ZINC001721751655 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721751655 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/863 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2nonc2c1) `ZINC001721751655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721751655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721751655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2nonc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 18, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 33, 18, 18, 24, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/864 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2nonc2c1) `ZINC001721751655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721751655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721751655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2nonc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 21, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 36, 21, 21, 26, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721751655 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 Building ZINC001721751655 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721751655 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 863) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2nonc2c1) `ZINC001721751655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721751655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721751655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2nonc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 18, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 33, 18, 18, 24, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 864) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2nonc2c1) `ZINC001721751655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721751655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721751655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2nonc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 21, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 36, 21, 21, 26, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721751655 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751655 Building ZINC001721751656 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721751656 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/865 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2nonc2c1) `ZINC001721751656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721751656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721751656 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2nonc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 21, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 36, 21, 21, 25, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/866 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2nonc2c1) `ZINC001721751656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721751656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721751656 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2nonc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 18, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 33, 18, 18, 24, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721751656 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 Building ZINC001721751656 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721751656 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 865) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2nonc2c1) `ZINC001721751656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721751656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721751656 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2nonc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 21, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 36, 21, 21, 25, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 866) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2nonc2c1) `ZINC001721751656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721751656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721751656 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2nonc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 18, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 33, 18, 18, 24, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721751656 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751656 Building ZINC001721751847 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721751847 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/867 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721751847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721751847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721751847 none Cc1sccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 14, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 41, 12, 12, 12, 9, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 41, 12, 9, 9, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/868 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721751847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721751847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721751847 none Cc1sccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 14, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 10, 10, 10, 9, 9, 7, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 44, 44, 10, 9, 9, 27, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721751847 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 Building ZINC001721751847 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721751847 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 867) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721751847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721751847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721751847 none Cc1sccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 14, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 41, 12, 12, 12, 9, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 41, 12, 9, 9, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 868) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721751847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721751847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721751847 none Cc1sccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 14, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 10, 10, 10, 9, 9, 7, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 44, 44, 10, 9, 9, 27, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721751847 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751847 Building ZINC001721751848 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721751848 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/869 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721751848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721751848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721751848 none Cc1sccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 14, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 10, 10, 10, 9, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 44, 44, 10, 9, 9, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/870 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721751848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721751848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721751848 none Cc1sccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 14, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 40, 12, 12, 12, 9, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 40, 40, 12, 9, 9, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721751848 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 Building ZINC001721751848 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721751848 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 869) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721751848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721751848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721751848 none Cc1sccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 14, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 10, 10, 10, 9, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 44, 44, 10, 9, 9, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 870) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721751848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721751848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721751848 none Cc1sccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 14, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 40, 12, 12, 12, 9, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 40, 40, 12, 9, 9, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721751848 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721751848 Building ZINC001721752057 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721752057 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/871 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 15, 15, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/872 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 12, 7, 5, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 12, 12, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/873 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/873' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 15, 15, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/874 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/874' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 12, 7, 5, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 12, 12, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752057 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 Building ZINC001721752057 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721752057 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 871) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 15, 15, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 872) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 12, 7, 5, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 12, 12, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 873) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 15, 15, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 874) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 12, 7, 5, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 12, 12, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752057 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 Building ZINC001721752057 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721752057 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 871) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 15, 15, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 872) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 12, 7, 5, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 12, 12, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 873) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 15, 15, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 874) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 12, 7, 5, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 12, 12, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752057 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 Building ZINC001721752057 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721752057 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 871) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 15, 15, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 872) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 12, 7, 5, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 12, 12, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 873) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 15, 15, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 874) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721752057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752057 none CO[C@H]1CC[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 12, 7, 5, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 12, 12, 21, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752057 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752057 Building ZINC001721752058 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721752058 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/875 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 13, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 13, 13, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/876 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 50, 17, 17, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/877 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/877' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 13, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 13, 13, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/878 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/878' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 50, 17, 17, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752058 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 Building ZINC001721752058 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721752058 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 875) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 13, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 13, 13, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 876) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 50, 17, 17, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 877) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 13, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 13, 13, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 878) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 50, 17, 17, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752058 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 Building ZINC001721752058 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721752058 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 875) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 13, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 13, 13, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 876) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 50, 17, 17, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 877) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 13, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 13, 13, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 878) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 50, 17, 17, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752058 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 Building ZINC001721752058 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001721752058 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 875) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 13, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 13, 13, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 876) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 50, 17, 17, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `2' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 2 (index: 877) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 50, 16, 16, 13, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 13, 13, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `3' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 3 (index: 878) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001721752058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001721752058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752058 none CO[C@H]1CC[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 50, 17, 17, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752058 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 2: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/2.* 3: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/3.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752058 Building ZINC001721752069 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752069 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/879 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752069 none CO[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 33, 35, 33, 33, 15, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 35, 35, 35, 33, 15, 15, 36, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 227 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/880 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752069 none CO[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 36, 38, 36, 36, 18, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 50, 50, 50, 38, 38, 38, 36, 18, 18, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 230 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752069 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 Building ZINC001721752069 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752069 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 879) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752069 none CO[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 33, 35, 33, 33, 15, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 35, 35, 35, 33, 15, 15, 36, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 227 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 880) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752069 none CO[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 36, 38, 36, 36, 18, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 50, 50, 50, 38, 38, 38, 36, 18, 18, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 230 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752069 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752069 Building ZINC001721752070 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752070 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/881 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752070 none CO[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 36, 39, 36, 36, 18, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 39, 39, 39, 36, 18, 18, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 232 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/882 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752070 none CO[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 33, 36, 33, 33, 16, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 36, 36, 36, 33, 16, 16, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 238 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752070 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 Building ZINC001721752070 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752070 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 881) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752070 none CO[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 36, 39, 36, 36, 18, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 39, 39, 39, 36, 18, 18, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 232 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 882) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752070 none CO[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 33, 36, 33, 33, 16, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 36, 36, 36, 33, 16, 16, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 238 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752070 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752070 Building ZINC001721752071 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752071 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/883 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752071 none CO[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 35, 39, 35, 35, 18, 15, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 39, 39, 39, 35, 18, 18, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 245 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/884 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752071 none CO[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 31, 32, 31, 31, 16, 11, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 32, 32, 32, 31, 16, 16, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752071 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 Building ZINC001721752071 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752071 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 883) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752071 none CO[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 35, 39, 35, 35, 18, 15, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 50, 50, 50, 39, 39, 39, 35, 18, 18, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 245 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 884) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752071 none CO[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 31, 32, 31, 31, 16, 11, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 32, 32, 32, 31, 16, 16, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752071 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752071 Building ZINC001721752072 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752072 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/885 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752072 none CO[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 31, 32, 31, 31, 16, 11, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 32, 32, 32, 31, 16, 16, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/886 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752072 none CO[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 36, 38, 36, 36, 17, 14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 50, 50, 50, 38, 38, 38, 36, 17, 17, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 240 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752072 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 Building ZINC001721752072 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752072 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 885) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752072 none CO[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 31, 32, 31, 31, 16, 11, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 32, 32, 32, 31, 16, 16, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 886) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1) `ZINC001721752072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752072 none CO[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 36, 38, 36, 36, 17, 14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 50, 50, 50, 38, 38, 38, 36, 17, 17, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 240 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752072 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752072 Building ZINC001721752111 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752111 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/887 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2occc2[nH]1) `ZINC001721752111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721752111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2occc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 27, 27, 27, 37, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 81, 37, 37, 47, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/888 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2occc2[nH]1) `ZINC001721752111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721752111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2occc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 21, 34, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 66, 34, 34, 47, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 264 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752111 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 Building ZINC001721752111 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752111 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 887) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2occc2[nH]1) `ZINC001721752111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721752111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2occc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 27, 27, 27, 37, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 81, 37, 37, 47, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 888) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2occc2[nH]1) `ZINC001721752111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721752111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2occc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 21, 34, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 66, 34, 34, 47, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 264 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752111 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752111 Building ZINC001721752112 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752112 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/889 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2occc2[nH]1) `ZINC001721752112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721752112 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2occc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 21, 34, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 66, 34, 34, 47, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 264 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/890 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2occc2[nH]1) `ZINC001721752112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721752112 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2occc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 27, 27, 27, 37, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 81, 37, 37, 47, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752112 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 Building ZINC001721752112 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752112 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 889) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2occc2[nH]1) `ZINC001721752112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721752112 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2occc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 21, 34, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 66, 34, 34, 47, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 264 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 890) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2occc2[nH]1) `ZINC001721752112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721752112 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2occc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 27, 27, 27, 37, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 81, 37, 37, 47, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752112 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752112 Building ZINC001721752433 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752433 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/891 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721752433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721752433 none Cc1ncccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 16, 16, 16, 13, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 16, 13, 13, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 234 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/892 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721752433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721752433 none Cc1ncccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 12, 12, 12, 10, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 41, 12, 10, 10, 15, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 199 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752433 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 Building ZINC001721752433 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752433 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 891) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721752433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721752433 none Cc1ncccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 16, 16, 16, 13, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 16, 13, 13, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 234 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 892) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721752433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721752433 none Cc1ncccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 12, 12, 12, 10, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 41, 12, 10, 10, 15, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 199 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752433 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752433 Building ZINC001721752434 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752434 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/893 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721752434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721752434 none Cc1ncccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 12, 12, 12, 9, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 12, 9, 9, 15, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 199 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/894 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721752434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721752434 none Cc1ncccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 15, 15, 15, 12, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 15, 12, 12, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 229 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752434 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 Building ZINC001721752434 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752434 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 893) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721752434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721752434 none Cc1ncccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 12, 12, 12, 9, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 12, 9, 9, 15, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 199 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 894) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721752434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721752434 none Cc1ncccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 15, 15, 15, 12, 9, 6, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 15, 12, 12, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 229 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752434 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752434 Building ZINC001721752445 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752445 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/895 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@H]1CCCCO1) `ZINC001721752445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752445 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 16, 22, 22, 22, 43, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 16, 16, 22, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 256 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/896 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@H]1CCCCO1) `ZINC001721752445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752445 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 9, 12, 17, 17, 17, 45, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 12, 12, 17, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 251 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752445 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 Building ZINC001721752445 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752445 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 895) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@H]1CCCCO1) `ZINC001721752445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752445 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 16, 22, 22, 22, 43, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 16, 16, 22, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 256 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 896) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@H]1CCCCO1) `ZINC001721752445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752445 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 9, 12, 17, 17, 17, 45, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 12, 12, 17, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 251 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752445 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752445 Building ZINC001721752446 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752446 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/897 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@@H]1CCCCO1) `ZINC001721752446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752446 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 19, 29, 29, 29, 48, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 19, 19, 29, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 256 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/898 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@@H]1CCCCO1) `ZINC001721752446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752446 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 13, 21, 21, 21, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 13, 13, 21, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752446 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 Building ZINC001721752446 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752446 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 897) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@@H]1CCCCO1) `ZINC001721752446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752446 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 19, 29, 29, 29, 48, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 19, 19, 29, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 256 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 898) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@@H]1CCCCO1) `ZINC001721752446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752446 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 13, 21, 21, 21, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 13, 13, 21, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752446 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752446 Building ZINC001721752447 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752447 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/899 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@H]1CCCCO1) `ZINC001721752447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752447 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 13, 21, 21, 21, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 13, 13, 21, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/900 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@H]1CCCCO1) `ZINC001721752447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752447 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 19, 28, 28, 28, 47, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 19, 19, 28, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 258 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752447 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 Building ZINC001721752447 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752447 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 899) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@H]1CCCCO1) `ZINC001721752447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752447 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 13, 21, 21, 21, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 13, 13, 21, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 900) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@H]1CCCCO1) `ZINC001721752447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752447 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 19, 28, 28, 28, 47, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 19, 19, 28, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 258 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752447 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752447 Building ZINC001721752448 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752448 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/901 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@@H]1CCCCO1) `ZINC001721752448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752448 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 9, 12, 17, 17, 17, 45, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 12, 12, 17, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 251 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/902 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@@H]1CCCCO1) `ZINC001721752448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752448 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 16, 22, 22, 22, 43, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 16, 16, 22, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 256 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752448 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 Building ZINC001721752448 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752448 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 901) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@@H]1CCCCO1) `ZINC001721752448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752448 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 9, 12, 17, 17, 17, 45, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 12, 12, 17, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 251 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 902) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@@H]1CCCCO1) `ZINC001721752448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001721752448 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 16, 22, 22, 22, 43, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 16, 16, 22, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 256 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752448 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752448 Building ZINC001721752737 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752737 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/903 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001721752737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721752737 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 22, 30, 30, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 45, 22, 22, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/904 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001721752737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721752737 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 11, 18, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752737 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 Building ZINC001721752737 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752737 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 903) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001721752737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721752737 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 22, 30, 30, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 45, 22, 22, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 904) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001721752737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721752737 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 11, 18, 34, 34, 35, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752737 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752737 Building ZINC001721752738 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752738 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/905 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001721752738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721752738 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 19, 36, 36, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 36, 19, 19, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 203 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/906 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001721752738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721752738 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 22, 32, 32, 38, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 42, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752738 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 Building ZINC001721752738 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752738 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 905) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001721752738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721752738 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 19, 36, 36, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 36, 19, 19, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 203 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 906) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001721752738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001721752738 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 22, 32, 32, 38, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 42, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752738 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752738 Building ZINC001721752764 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752764 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/907 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCCn1cccc1) `ZINC001721752764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752764 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCCn1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 9, 12, 12, 12, 41, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 9, 9, 12, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 281 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/908 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCCn1cccc1) `ZINC001721752764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752764 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCCn1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 9, 15, 15, 15, 45, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 21, 9, 9, 15, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 281 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752764 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 Building ZINC001721752764 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752764 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 907) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCCn1cccc1) `ZINC001721752764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752764 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCCn1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 9, 12, 12, 12, 41, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 9, 9, 12, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 281 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 908) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCCn1cccc1) `ZINC001721752764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752764 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCCn1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 9, 15, 15, 15, 45, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 21, 9, 9, 15, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 281 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752764 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752764 Building ZINC001721752765 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752765 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/909 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCCn1cccc1) `ZINC001721752765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752765 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCCn1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 9, 15, 15, 15, 45, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 21, 9, 9, 15, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 281 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/910 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCCn1cccc1) `ZINC001721752765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752765 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCCn1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 9, 12, 12, 12, 41, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 9, 9, 12, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 281 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752765 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 Building ZINC001721752765 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752765 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 909) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCCn1cccc1) `ZINC001721752765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752765 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCCn1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 9, 15, 15, 15, 45, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 21, 9, 9, 15, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 281 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 910) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCCn1cccc1) `ZINC001721752765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721752765 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCCn1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 9, 12, 12, 12, 41, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 9, 9, 12, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 281 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752765 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752765 Building ZINC001721752970 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752970 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/911 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2nc[nH]c21) `ZINC001721752970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721752970 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2nc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 28, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 48, 28, 28, 39, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/912 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2nc[nH]c21) `ZINC001721752970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721752970 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2nc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 17, 33, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 51, 33, 33, 41, 50, 50, 50, 49] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 253 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752970 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 Building ZINC001721752970 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752970 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 911) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2nc[nH]c21) `ZINC001721752970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721752970 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2nc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 28, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 48, 28, 28, 39, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 912) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2nc[nH]c21) `ZINC001721752970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721752970 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2nc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 17, 33, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 51, 33, 33, 41, 50, 50, 50, 49] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 253 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752970 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752970 Building ZINC001721752971 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752971 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/913 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2nc[nH]c21) `ZINC001721752971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721752971 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2nc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 17, 31, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 51, 31, 31, 40, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 252 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/914 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2nc[nH]c21) `ZINC001721752971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721752971 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2nc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 28, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 48, 28, 28, 39, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752971 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 Building ZINC001721752971 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721752971 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 913) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2nc[nH]c21) `ZINC001721752971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721752971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721752971 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2nc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 17, 31, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 51, 31, 31, 40, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 252 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 914) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2nc[nH]c21) `ZINC001721752971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721752971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721752971 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2nc[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 28, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 48, 28, 28, 39, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721752971 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721752971 Building ZINC001721753000 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753000 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/915 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2cccn2cn1) `ZINC001721753000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721753000 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2cccn2cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 29, 29, 29, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 87, 40, 40, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 309 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/916 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2cccn2cn1) `ZINC001721753000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721753000 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2cccn2cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 23, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 72, 37, 37, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 278 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753000 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 Building ZINC001721753000 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753000 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 915) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2cccn2cn1) `ZINC001721753000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721753000 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2cccn2cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 29, 29, 29, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 87, 40, 40, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 309 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 916) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2cccn2cn1) `ZINC001721753000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721753000 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2cccn2cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 23, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 72, 37, 37, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 278 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753000 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753000 Building ZINC001721753001 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753001 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/917 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2cccn2cn1) `ZINC001721753001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721753001 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2cccn2cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 25, 25, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 75, 38, 38, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/918 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2cccn2cn1) `ZINC001721753001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721753001 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2cccn2cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 29, 29, 29, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 87, 40, 40, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 309 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753001 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 Building ZINC001721753001 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753001 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 917) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2cccn2cn1) `ZINC001721753001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721753001 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2cccn2cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 25, 25, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 75, 38, 38, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 918) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2cccn2cn1) `ZINC001721753001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721753001 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2cccn2cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 29, 29, 29, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 87, 40, 40, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 309 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753001 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753001 Building ZINC001721753046 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753046 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/919 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCc1ccccn1) `ZINC001721753046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753046 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 9, 16, 21, 21, 21, 39, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 16, 16, 21, 39, 39, 45, 45, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 239 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/920 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCc1ccccn1) `ZINC001721753046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753046 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 11, 17, 17, 17, 37, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 21, 11, 11, 17, 37, 37, 44, 44, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 223 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753046 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 Building ZINC001721753046 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753046 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 919) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCc1ccccn1) `ZINC001721753046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753046 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 9, 16, 21, 21, 21, 39, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 16, 16, 21, 39, 39, 45, 45, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 239 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 920) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCc1ccccn1) `ZINC001721753046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753046 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CCc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 11, 17, 17, 17, 37, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 21, 11, 11, 17, 37, 37, 44, 44, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 223 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753046 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753046 Building ZINC001721753047 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753047 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/921 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCc1ccccn1) `ZINC001721753047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753047 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 11, 17, 17, 17, 37, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 21, 11, 11, 17, 37, 37, 44, 44, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 223 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/922 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/922' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCc1ccccn1) `ZINC001721753047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753047 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 9, 15, 21, 21, 21, 40, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 15, 15, 21, 40, 40, 45, 45, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 237 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753047 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 Building ZINC001721753047 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753047 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 921) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCc1ccccn1) `ZINC001721753047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753047 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 11, 17, 17, 17, 37, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 21, 11, 11, 17, 37, 37, 44, 44, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 223 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 922) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCc1ccccn1) `ZINC001721753047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753047 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CCc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 9, 15, 21, 21, 21, 40, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 15, 15, 21, 40, 40, 45, 45, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 237 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753047 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753047 Building ZINC001721753064 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753064 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/923 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)c1) `ZINC001721753064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753064 none Cc1cnc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 41, 41, 41, 27, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 41, 27, 27, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/924 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)c1) `ZINC001721753064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753064 none Cc1cnc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 47, 47, 31, 19, 9, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 31, 31, 57, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 263 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753064 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 Building ZINC001721753064 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753064 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 923) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)c1) `ZINC001721753064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753064 none Cc1cnc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 41, 41, 41, 27, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 41, 27, 27, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 924) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)c1) `ZINC001721753064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753064 none Cc1cnc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 47, 47, 31, 19, 9, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 31, 31, 57, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 263 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753064 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753064 Building ZINC001721753065 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753065 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/925 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)c1) `ZINC001721753065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753065 none Cc1cnc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 47, 47, 31, 19, 9, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 31, 31, 57, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 263 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/926 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/926' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)c1) `ZINC001721753065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753065 none Cc1cnc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 40, 40, 40, 26, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 26, 26, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753065 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 Building ZINC001721753065 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753065 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 925) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)c1) `ZINC001721753065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753065 none Cc1cnc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 47, 47, 31, 19, 9, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 31, 31, 57, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 263 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 926) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)c1) `ZINC001721753065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753065 none Cc1cnc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 40, 40, 40, 26, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 26, 26, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753065 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753065 Building ZINC001721753154 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753154 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/927 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1CCCOCC1) `ZINC001721753154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753154 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 10, 10, 10, 17, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 17, 17, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 215 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/928 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1CCCOCC1) `ZINC001721753154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753154 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 10, 10, 10, 15, 18, 18, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 15, 15, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753154 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 Building ZINC001721753154 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753154 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 927) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1CCCOCC1) `ZINC001721753154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753154 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 10, 10, 10, 17, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 17, 17, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 215 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 928) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1CCCOCC1) `ZINC001721753154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753154 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 10, 10, 10, 15, 18, 18, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 15, 15, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753154 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753154 Building ZINC001721753155 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753155 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/929 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CCCOCC1) `ZINC001721753155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753155 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 13, 17, 17, 32, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 13, 13, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/930 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CCCOCC1) `ZINC001721753155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753155 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 13, 18, 18, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 27, 13, 13, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753155 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 Building ZINC001721753155 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753155 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 929) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CCCOCC1) `ZINC001721753155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753155 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 13, 17, 17, 32, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 13, 13, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 930) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CCCOCC1) `ZINC001721753155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753155 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 13, 18, 18, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 27, 13, 13, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753155 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753155 Building ZINC001721753156 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753156 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/931 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CCCOCC1) `ZINC001721753156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753156 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 11, 17, 17, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 11, 11, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/932 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CCCOCC1) `ZINC001721753156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753156 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 7, 7, 7, 13, 16, 16, 32, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 21, 13, 13, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753156 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 Building ZINC001721753156 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753156 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 931) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CCCOCC1) `ZINC001721753156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753156 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 11, 17, 17, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 11, 11, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 932) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CCCOCC1) `ZINC001721753156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753156 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 7, 7, 7, 13, 16, 16, 32, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 21, 13, 13, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753156 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753156 Building ZINC001721753157 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753157 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/933 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1CCCOCC1) `ZINC001721753157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753157 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 14, 19, 19, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 27, 14, 14, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/934 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/934' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1CCCOCC1) `ZINC001721753157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753157 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 16, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 16, 16, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753157 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 Building ZINC001721753157 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753157 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 933) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1CCCOCC1) `ZINC001721753157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753157 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 14, 19, 19, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 27, 14, 14, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 934) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1CCCOCC1) `ZINC001721753157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753157 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1CCCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 16, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 16, 16, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753157 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753157 Building ZINC001721753414 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753414 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/935 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)N1CCCC1) `ZINC001721753414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721753414 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 16, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 258 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/936 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)N1CCCC1) `ZINC001721753414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721753414 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 22, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 45, 22, 22, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 263 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753414 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 Building ZINC001721753414 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753414 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 935) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)N1CCCC1) `ZINC001721753414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721753414 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 16, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 258 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 936) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)N1CCCC1) `ZINC001721753414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721753414 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 22, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 45, 22, 22, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 263 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753414 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753414 Building ZINC001721753415 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753415 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/937 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)N1CCCC1) `ZINC001721753415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721753415 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 22, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 45, 22, 22, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 263 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/938 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)N1CCCC1) `ZINC001721753415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721753415 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 16, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 258 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753415 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 Building ZINC001721753415 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753415 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 937) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)N1CCCC1) `ZINC001721753415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721753415 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 22, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 45, 22, 22, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 263 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 938) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)N1CCCC1) `ZINC001721753415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001721753415 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 16, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 258 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753415 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753415 Building ZINC001721753438 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753438 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/939 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721753438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721753438 none C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 50, 42, 42, 31, 19, 11, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 31, 31, 57, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 275 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/940 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721753438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721753438 none C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 37, 50, 37, 37, 24, 12, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 24, 24, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 256 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753438 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 Building ZINC001721753438 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753438 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 939) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721753438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721753438 none C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 50, 42, 42, 31, 19, 11, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 31, 31, 57, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 275 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 940) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721753438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721753438 none C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 37, 50, 37, 37, 24, 12, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 24, 24, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 256 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753438 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753438 Building ZINC001721753439 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753439 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/941 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721753439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721753439 none C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 50, 33, 33, 24, 12, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 24, 23, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 269 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/942 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721753439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721753439 none C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 50, 41, 41, 30, 18, 11, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 30, 30, 54, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 276 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753439 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 Building ZINC001721753439 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753439 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 941) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721753439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721753439 none C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 50, 33, 33, 24, 12, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 24, 23, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 269 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 942) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC001721753439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001721753439 none C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 41, 50, 41, 41, 30, 18, 11, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 30, 30, 54, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 276 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753439 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753439 Building ZINC001721753464 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753464 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/943 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721753464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753464 none CC[C@@H]1CCO[C@@H]1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 50, 43, 43, 24, 15, 10, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 24, 24, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 243 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/944 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721753464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753464 none CC[C@@H]1CCO[C@@H]1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 41, 41, 22, 14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 22, 22, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 240 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753464 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 Building ZINC001721753464 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753464 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 943) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721753464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753464 none CC[C@@H]1CCO[C@@H]1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 50, 43, 43, 24, 15, 10, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 24, 24, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 243 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 944) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721753464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753464 none CC[C@@H]1CCO[C@@H]1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 50, 41, 41, 22, 14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 22, 22, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 240 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753464 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753464 Building ZINC001721753465 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753465 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/945 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721753465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753465 none CC[C@@H]1CCO[C@@H]1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 50, 40, 40, 19, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 19, 19, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 236 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/946 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721753465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753465 none CC[C@@H]1CCO[C@@H]1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 42, 50, 41, 41, 23, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 23, 23, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 240 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753465 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 Building ZINC001721753465 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753465 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 945) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721753465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753465 none CC[C@@H]1CCO[C@@H]1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 50, 40, 40, 19, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 19, 19, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 236 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 946) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721753465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721753465 none CC[C@@H]1CCO[C@@H]1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 42, 50, 41, 41, 23, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 23, 23, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 240 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753465 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753465 Building ZINC001721753470 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753470 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/947 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753470 none C[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 30, 43, 30, 30, 22, 15, 10, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 43, 43, 43, 30, 22, 22, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 256 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/948 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753470 none C[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 33, 48, 33, 33, 21, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 48, 48, 48, 33, 21, 21, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 265 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753470 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 Building ZINC001721753470 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753470 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 947) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753470 none C[C@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 30, 43, 30, 30, 22, 15, 10, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 43, 43, 43, 30, 22, 22, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 256 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 948) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753470 none C[C@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 33, 48, 33, 33, 21, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 48, 48, 48, 33, 21, 21, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 265 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753470 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753470 Building ZINC001721753471 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753471 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/949 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753471 none C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 34, 49, 34, 34, 21, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 34, 21, 21, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 267 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/950 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753471 none C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 40, 26, 26, 20, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 26, 20, 20, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753471 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 Building ZINC001721753471 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753471 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 949) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753471 none C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 34, 49, 34, 34, 21, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 34, 21, 21, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 267 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 950) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753471 none C[C@@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 40, 26, 26, 20, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 26, 20, 20, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753471 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753471 Building ZINC001721753472 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753472 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/951 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753472 none C[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 23, 36, 23, 23, 19, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 36, 36, 36, 23, 19, 19, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 247 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/952 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753472 none C[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 40, 26, 26, 23, 14, 10, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 26, 23, 23, 42, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 253 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753472 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 Building ZINC001721753472 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753472 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 951) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753472 none C[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 23, 36, 23, 23, 19, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 36, 36, 36, 23, 19, 19, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 247 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 952) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753472 none C[C@H](C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 40, 26, 26, 23, 14, 10, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 26, 23, 23, 42, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 253 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753472 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753472 Building ZINC001721753473 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753473 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/953 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753473 none C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 40, 26, 26, 23, 14, 10, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 26, 23, 23, 42, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 253 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/954 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753473 none C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 24, 36, 24, 24, 19, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 36, 36, 36, 24, 19, 19, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 245 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753473 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 Building ZINC001721753473 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753473 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 953) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753473 none C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 40, 26, 26, 23, 14, 10, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 26, 23, 23, 42, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 253 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 954) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1) `ZINC001721753473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721753473 none C[C@@H](C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 24, 36, 24, 24, 19, 12, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 36, 36, 36, 24, 19, 19, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 245 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753473 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753473 Building ZINC001721753506 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753506 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/955 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1c[nH]nc1C1CC1) `ZINC001721753506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721753506 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1c[nH]nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 11, 21, 21, 21, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 11, 11, 21, 49, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/956 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1c[nH]nc1C1CC1) `ZINC001721753506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721753506 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1c[nH]nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 15, 24, 24, 24, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 30, 15, 15, 24, 49, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753506 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 Building ZINC001721753506 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753506 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 955) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1c[nH]nc1C1CC1) `ZINC001721753506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721753506 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1c[nH]nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 11, 21, 21, 21, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 11, 11, 21, 49, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 956) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1c[nH]nc1C1CC1) `ZINC001721753506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721753506 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1c[nH]nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 15, 24, 24, 24, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 30, 15, 15, 24, 49, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753506 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753506 Building ZINC001721753507 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753507 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/957 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1c[nH]nc1C1CC1) `ZINC001721753507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721753507 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1c[nH]nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 15, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 33, 15, 15, 20, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/958 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1c[nH]nc1C1CC1) `ZINC001721753507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721753507 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1c[nH]nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 13, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 13, 13, 22, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753507 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 Building ZINC001721753507 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753507 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 957) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1c[nH]nc1C1CC1) `ZINC001721753507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721753507 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1c[nH]nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 15, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 33, 15, 15, 20, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 958) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1c[nH]nc1C1CC1) `ZINC001721753507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721753507 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1c[nH]nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 13, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 13, 13, 22, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753507 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753507 Building ZINC001721753554 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753554 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/959 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(C(F)(F)F)CC1) `ZINC001721753554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721753554 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 15, 23, 37, 37, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 48, 23, 23, 37, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 248 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/960 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(C(F)(F)F)CC1) `ZINC001721753554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721753554 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 29, 35, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 51, 29, 29, 35, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 265 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753554 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 Building ZINC001721753554 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753554 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 959) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(C(F)(F)F)CC1) `ZINC001721753554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721753554 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 15, 23, 37, 37, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 48, 23, 23, 37, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 248 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 960) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(C(F)(F)F)CC1) `ZINC001721753554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721753554 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 29, 35, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 51, 29, 29, 35, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 265 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753554 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753554 Building ZINC001721753555 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753555 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/961 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(C(F)(F)F)CC1) `ZINC001721753555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721753555 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 15, 26, 34, 34, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 45, 26, 26, 34, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 252 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/962 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/962' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(C(F)(F)F)CC1) `ZINC001721753555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721753555 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 13, 20, 35, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 42, 20, 20, 35, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 241 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753555 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 Building ZINC001721753555 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721753555 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 961) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(C(F)(F)F)CC1) `ZINC001721753555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721753555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721753555 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 15, 26, 34, 34, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 45, 26, 26, 34, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 252 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 962) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(C(F)(F)F)CC1) `ZINC001721753555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721753555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001721753555 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 13, 20, 35, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 42, 20, 20, 35, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 241 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721753555 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721753555 Building ZINC001721818062 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818062 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/963 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001721818062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721818062 none CCn1cc(CC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 33, 33, 33, 26, 19, 19, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 50, 50, 50, 50, 50, 37, 37, 37, 33, 26, 26, 19, 19, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/964 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001721818062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721818062 none CCn1cc(CC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 36, 36, 36, 27, 19, 19, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50, 50, 50, 50, 39, 39, 39, 36, 27, 27, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818062 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 Building ZINC001721818062 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818062 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 963) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001721818062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721818062 none CCn1cc(CC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 33, 33, 33, 26, 19, 19, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 50, 50, 50, 50, 50, 37, 37, 37, 33, 26, 26, 19, 19, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 964) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001721818062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001721818062 none CCn1cc(CC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 36, 36, 36, 27, 19, 19, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50, 50, 50, 50, 39, 39, 39, 36, 27, 27, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818062 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818062 Building ZINC001721818204 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818204 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/965 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CCN1CCOCC1) `ZINC001721818204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818204 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 19, 21, 21, 21, 43, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 19, 19, 21, 43, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/966 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CCN1CCOCC1) `ZINC001721818204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818204 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 18, 21, 21, 21, 43, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 18, 18, 21, 43, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818204 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 Building ZINC001721818204 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818204 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 965) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CCN1CCOCC1) `ZINC001721818204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818204 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 19, 21, 21, 21, 43, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 19, 19, 21, 43, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 966) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CCN1CCOCC1) `ZINC001721818204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818204 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 18, 21, 21, 21, 43, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 18, 18, 21, 43, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818204 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818204 Building ZINC001721818241 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818241 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/967 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721818241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818241 none CN1C(=O)CCC[C@@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 48, 48, 37, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 37, 37, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/968 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721818241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818241 none CN1C(=O)CCC[C@@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 49, 49, 37, 27, 27, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 37, 37, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818241 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 Building ZINC001721818241 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818241 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 967) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721818241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818241 none CN1C(=O)CCC[C@@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 48, 48, 37, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 37, 37, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 968) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721818241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818241 none CN1C(=O)CCC[C@@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 49, 49, 37, 27, 27, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 37, 37, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818241 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818241 Building ZINC001721818244 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818244 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/969 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721818244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818244 none CN1C(=O)CCC[C@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 49, 49, 37, 27, 27, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 37, 37, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/970 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721818244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818244 none CN1C(=O)CCC[C@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 48, 48, 37, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 37, 37, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818244 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 Building ZINC001721818244 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818244 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 969) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721818244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818244 none CN1C(=O)CCC[C@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 49, 49, 37, 27, 27, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 37, 37, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 970) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721818244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818244 none CN1C(=O)CCC[C@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 50, 48, 48, 37, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 37, 37, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818244 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818244 Building ZINC001721818389 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818389 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/971 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2n[nH]cc2C1) `ZINC001721818389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818389 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 32, 38, 38, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 21, 21, 32, 32, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/972 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/972' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2n[nH]cc2C1) `ZINC001721818389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818389 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 28, 28, 33, 37, 37, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 28, 28, 33, 33, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818389 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 Building ZINC001721818389 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818389 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 971) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2n[nH]cc2C1) `ZINC001721818389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818389 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 32, 38, 38, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 21, 21, 32, 32, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 972) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2n[nH]cc2C1) `ZINC001721818389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818389 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 28, 28, 33, 37, 37, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 28, 28, 33, 33, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818389 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818389 Building ZINC001721818392 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818392 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/973 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2n[nH]cc2C1) `ZINC001721818392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818392 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 30, 30, 35, 40, 40, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 30, 30, 35, 35, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/974 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2n[nH]cc2C1) `ZINC001721818392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818392 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 22, 22, 34, 40, 40, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 34, 34, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818392 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 Building ZINC001721818392 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818392 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 973) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2n[nH]cc2C1) `ZINC001721818392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818392 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 30, 30, 35, 40, 40, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 30, 30, 35, 35, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 974) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2n[nH]cc2C1) `ZINC001721818392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721818392 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 22, 22, 34, 40, 40, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 34, 34, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818392 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818392 Building ZINC001721818456 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818456 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/975 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cccnc1C(N)=O) `ZINC001721818456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818456 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cccnc1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 20, 20, 29, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 20, 20, 29, 29, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/976 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/976' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cccnc1C(N)=O) `ZINC001721818456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818456 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cccnc1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 20, 20, 29, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 20, 20, 29, 29, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818456 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 Building ZINC001721818456 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818456 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 975) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cccnc1C(N)=O) `ZINC001721818456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818456 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cccnc1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 20, 20, 29, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 20, 20, 29, 29, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 976) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cccnc1C(N)=O) `ZINC001721818456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818456 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cccnc1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 20, 20, 29, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 20, 20, 29, 29, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818456 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818456 Building ZINC001721818524 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818524 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/977 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CNC(=O)c1ccco1) `ZINC001721818524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721818524 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CNC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 16, 20, 20, 20, 47, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 16, 16, 20, 47, 47, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/978 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CNC(=O)c1ccco1) `ZINC001721818524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721818524 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CNC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 18, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 18, 18, 22, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818524 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 Building ZINC001721818524 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818524 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 977) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CNC(=O)c1ccco1) `ZINC001721818524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721818524 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CNC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 16, 20, 20, 20, 47, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 16, 16, 20, 47, 47, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 978) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CNC(=O)c1ccco1) `ZINC001721818524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721818524 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CNC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 18, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 18, 18, 22, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818524 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818524 Building ZINC001721818817 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818817 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/979 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cn1ccccc1=O) `ZINC001721818817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818817 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 20, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 13, 13, 20, 20, 25, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/980 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/980' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cn1ccccc1=O) `ZINC001721818817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818817 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 19, 25, 25, 25, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 13, 13, 19, 19, 25, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818817 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 Building ZINC001721818817 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818817 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 979) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cn1ccccc1=O) `ZINC001721818817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818817 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 20, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 13, 13, 20, 20, 25, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 980) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cn1ccccc1=O) `ZINC001721818817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818817 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 19, 25, 25, 25, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 13, 13, 19, 19, 25, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818817 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818817 Building ZINC001721818835 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818835 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/981 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CN2CCC1CC2) `ZINC001721818835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818835 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CN2CCC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 24, 24, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/982 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CN2CCC1CC2) `ZINC001721818835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818835 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CN2CCC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 20, 20, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818835 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 Building ZINC001721818835 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818835 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 981) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CN2CCC1CC2) `ZINC001721818835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818835 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CN2CCC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 24, 24, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 982) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CN2CCC1CC2) `ZINC001721818835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818835 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CN2CCC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 20, 20, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818835 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818835 Building ZINC001721818836 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818836 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/983 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CN2CCC1CC2) `ZINC001721818836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818836 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CN2CCC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 20, 20, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/984 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CN2CCC1CC2) `ZINC001721818836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818836 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CN2CCC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 23, 23, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818836 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 Building ZINC001721818836 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818836 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 983) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CN2CCC1CC2) `ZINC001721818836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818836 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CN2CCC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 20, 20, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 984) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CN2CCC1CC2) `ZINC001721818836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001721818836 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CN2CCC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 7, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 23, 23, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818836 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818836 Building ZINC001721818843 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818843 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/985 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721818843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818843 none Cn1c(=O)cccc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 37, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 37, 37, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/986 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721818843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818843 none Cn1c(=O)cccc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 35, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 44, 35, 35, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818843 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 Building ZINC001721818843 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818843 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 985) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721818843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818843 none Cn1c(=O)cccc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 37, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 37, 37, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 986) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721818843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721818843 none Cn1c(=O)cccc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 35, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 44, 35, 35, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818843 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818843 Building ZINC001721818971 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818971 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/987 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(OCC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001721818971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721818971 none Cn1cc(OCC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 49, 49, 42, 29, 29, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 49, 42, 42, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/988 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/988' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(OCC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001721818971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721818971 none Cn1cc(OCC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 49, 49, 42, 29, 29, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 49, 42, 42, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818971 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 Building ZINC001721818971 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721818971 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 987) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(OCC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001721818971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721818971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721818971 none Cn1cc(OCC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 49, 49, 42, 29, 29, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 49, 42, 42, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 988) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(OCC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001721818971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721818971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721818971 none Cn1cc(OCC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 49, 49, 42, 29, 29, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 49, 42, 42, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721818971 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721818971 Building ZINC001721819105 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721819105 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/989 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2c[nH]nc2C1) `ZINC001721819105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721819105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721819105 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2c[nH]nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 30, 30, 34, 43, 43, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 30, 30, 34, 34, 43, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/990 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/990' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2c[nH]nc2C1) `ZINC001721819105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721819105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721819105 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2c[nH]nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 26, 26, 38, 45, 45, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 26, 26, 38, 38, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721819105 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 Building ZINC001721819105 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721819105 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 989) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2c[nH]nc2C1) `ZINC001721819105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721819105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721819105 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2c[nH]nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 30, 30, 34, 43, 43, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 30, 30, 34, 34, 43, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 990) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2c[nH]nc2C1) `ZINC001721819105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721819105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721819105 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@H]1CCc2c[nH]nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 26, 26, 38, 45, 45, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 26, 26, 38, 38, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721819105 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819105 Building ZINC001721819108 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721819108 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/991 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2c[nH]nc2C1) `ZINC001721819108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721819108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721819108 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2c[nH]nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 39, 45, 45, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 27, 39, 39, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/992 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2c[nH]nc2C1) `ZINC001721819108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721819108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721819108 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2c[nH]nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 38, 43, 43, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 28, 28, 38, 38, 43, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721819108 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 Building ZINC001721819108 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721819108 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 991) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2c[nH]nc2C1) `ZINC001721819108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721819108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721819108 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2c[nH]nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 39, 45, 45, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 27, 39, 39, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 992) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2c[nH]nc2C1) `ZINC001721819108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721819108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001721819108 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)[C@@H]1CCc2c[nH]nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 38, 43, 43, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 28, 28, 38, 38, 43, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721819108 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819108 Building ZINC001721819496 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721819496 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/993 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ncccc12) `ZINC001721819496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721819496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721819496 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 24, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/994 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ncccc12) `ZINC001721819496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721819496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721819496 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721819496 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 Building ZINC001721819496 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721819496 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 993) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ncccc12) `ZINC001721819496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721819496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721819496 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 24, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 994) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ncccc12) `ZINC001721819496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721819496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001721819496 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721819496 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721819496 Building ZINC001721912950 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721912950 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/995 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721912950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721912950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721912950 none C[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 18, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 41, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/996 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721912950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721912950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721912950 none C[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 19, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 37, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721912950 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 Building ZINC001721912950 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721912950 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 995) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721912950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721912950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721912950 none C[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 18, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 41, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 996) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721912950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721912950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001721912950 none C[C@H](CNC(=O)c1cnn2ccncc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 19, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 37, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721912950 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912950 Building ZINC001721912977 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721912977 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/997 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CNC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721912977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721912977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721912977 none C[C@H](CNC(=O)CNC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 16, 16, 16, 31, 40, 40, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 16, 31, 31, 40, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/998 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CNC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721912977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721912977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721912977 none C[C@H](CNC(=O)CNC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 14, 27, 27, 27, 38, 48, 49, 48, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 27, 38, 38, 49, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 208 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721912977 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 Building ZINC001721912977 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721912977 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 997) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CNC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721912977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721912977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721912977 none C[C@H](CNC(=O)CNC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 16, 16, 16, 31, 40, 40, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 16, 31, 31, 40, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 998) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CNC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721912977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721912977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001721912977 none C[C@H](CNC(=O)CNC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 14, 27, 27, 27, 38, 48, 49, 48, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 27, 38, 38, 49, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 208 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721912977 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912977 Building ZINC001721912980 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721912980 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/999 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cc2c(cn1)OCCO2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721912980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721912980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721912980 none C[C@H](CNC(=O)c1cc2c(cn1)OCCO2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 24, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 48, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/340664/xdr-8058097.96/working/3D/1000 `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/1000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cc2c(cn1)OCCO2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721912980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721912980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721912980 none C[C@H](CNC(=O)c1cc2c(cn1)OCCO2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 24, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 47, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721912980 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 Building ZINC001721912980 mkdir: created directory `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001721912980 mkdir: created directory `0' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/0 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 0 (index: 999) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cc2c(cn1)OCCO2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001721912980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001721912980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721912980 none C[C@H](CNC(=O)c1cc2c(cn1)OCCO2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 24, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 48, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 mkdir: created directory `1' /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/1 /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Protomer 1 (index: 1000) grep: /scratch/xiaobo/340664/xdr-8058097.96/working/3D/1000: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cc2c(cn1)OCCO2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001721912980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001721912980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001721912980 none C[C@H](CNC(=O)c1cc2c(cn1)OCCO2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 24, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 47, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Finished preparing ZINC001721912980 Recording results /scratch/xiaobo/340664/xdr-8058097.96/working /scratch/xiaobo/340664/xdr-8058097.96 Appending to /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.* 0: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/0.* 1: /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980/1.* Removing working files in /scratch/xiaobo/340664/xdr-8058097.96/working/building/ZINC001721912980 /scratch/xiaobo/340664/xdr-8058097.96 Compressing combined databse files /scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/340664/xdr-8058097.96/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/340664/xdr-8058097.96/working/3D/1001' removed directory: `/scratch/xiaobo/340664/xdr-8058097.96/working/3D' rmdir: removing directory, `/scratch/xiaobo/340664/xdr-8058097.96/working/building' rmdir: removing directory, `/scratch/xiaobo/340664/xdr-8058097.96/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/logs `/scratch/xiaobo/340664/xdr-8058097.96' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xdr' `/scratch/xiaobo/340664/xdr-8058097.96/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xdr/finished' `/scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xdr/finished/xdr.db2.gz' removed `/scratch/xiaobo/340664/xdr-8058097.96/finished/xdr.db2.gz' removed directory: `/scratch/xiaobo/340664/xdr-8058097.96/finished' removed directory: `/scratch/xiaobo/340664/xdr-8058097.96'